Pakistan’s Domestic Issues Are Just as Grave as Taliban Conflict

Deadly clashes with the Afghan Taliban have put Islamabad in the spotlight, but internal unrest may present a greater risk.

In recent weeks, deadly clashes between the Pakistani military and the Afghan Taliban have drawn international attention. Since the Taliban’s return to power in 2021, relations have greatly deteriorated between Islamabad and Kabul, disrupting what had previously been a mutually beneficial relationship between the pair. Pakistan is now in the unenviable position of having traded missile strikes with three of its immediate neighbors since the start of last year. Yet, Pakistan faces a potentially graver threat from within. Domestic protests throughout the latter half of 2025 have underscored the vulnerable position the government in Islamabad currently occupies, suggesting that its demise could come at the hands of its own population, rather than an external military power.

A central theme of government overreach has been the thread connecting various strikes, demonstrations, and protests that have gripped Gilgit Baltistan, Pakistan-administered Kashmir, and Khyber Pakhtunkhwa in recent months. These issues came to a head in the final week of September, with some lingering into early October. In July, Islamabad had attempted to expand its revenue base, bypassing Gilgit Baltistan’s historical exemption from direct taxation, owing to the region’s unresolved status and exclusion from Pakistan’s constitutional framework. This bold move, however, swiftly backfired, as local traders initiated a sit-in protest at the region’s Sost Dry Port, opposing the Federal Board of Revenue’s attempt to impose taxes on imported goods. This is not the first time the Federal Board of Revenue has attempted to extract taxes from the region, though every attempt has similarly met public anger.

After a more than two-month-long standoff, Islamabad finally backed down, reaching an agreement with protestors. In that time, however, the Karakoram Highway, the vital land connection between Pakistan and China, was brought to a complete standstill, suspending trade between the two countries and even preventing Chinese tourists from returning home. In some cases, Chinese citizens stranded in Pakistan staged anti-government protests of their own. The economic consequences of the protest are evident: trade and tourism are essential to the local economy in Gilgit Baltistan, and, more broadly, Pakistan’s trade links with China are an essential feature of the pair’s bilateral relationship. Symbolically, events in Gilgit Baltistan could prove even more damaging for Islamabad in the long term. This most recent attempt to impose taxes on locals in the region has reopened conversations about the region’s political future, with complaints of “no taxation without representation” gaining momentum. Beijing will also undoubtedly be concerned at Pakistan’s apparent inability to keep open a major artery of the China-Pakistan Economic Corridor (CPEC).

Meanwhile, as the government grappled with matters in Gilgit Baltistan a new front of domestic unrest was opening in Pakistan-administered Kashmir. On Sept. 29, a local civil rights organization, the Awami Action Committee (AAC), led a widespread protest against the government in Islamabad. Bearing similarities to the underlying complaints voiced in Gilgit Baltistan, locals in Pakistan-administered Kashmir expressed their discontent at perceived government exploitation. Home to the Mangla Dam and Neelum-Jhelum Hydroelectric Project, Pakistan-administered Kashmir is a major hydropower hub for the whole of Pakistan. Yet despite this, residents claim to have not felt the economic benefits that such projects are reaping and are instead suffering from frequent power blackouts and increasing bills. This, along with broader food inflation and the country’s broader economic difficulties, forced locals onto the streets to protest the central government.

Unlike in Gilgit Baltistan, however, protestors in Pakistan-administered Kashmir were met with a show of force from Pakistani security forces, who employed a typically heavy-handed response. Clashes between police and protestors resulted in at least 10 deaths, including three police officers. Islamabad also imposed a communications blackout, which, alongside civilian deaths, attracted the ire of human rights groups. Complaints of resource extraction by the central government without sufficient reinvestment also mirror the longstanding dispute between Islamabad and the province of Balochistan.

Islamabad also imposed a communications blackout, which alongside civilian deaths attracted the ire of human rights groups.

During the first week of October, the AAC achieved a breakthrough with the local government, which agreed to continue subsidizing electricity and wheat. The resolution was brought about thanks to direct intervention from Islamabad, with Prime Minister Shehbaz Sharif dispatching a delegation to Muzaffarabad to hold talks with the AAC and local politicians. The country’s federal minister subsequently praised the outcome on X, although this clash has severely weakened Islamabad’s position in the region. As with Gilgit Baltistan, issues over political representation have now returned to the fore in Pakistan-administered Kashmir, which could prove problematic in the near future. For now, peace in the region remains tenuous, and it is unclear whether the local government can maintain its promised subsidies indefinitely. If such economic support becomes untenable, then the chances of another flare-up remain high.

Moving west, Khyber Pakhtunkhwa has come under much attention in October as the stage of skirmishes between the Pakistani military and the Afghan Taliban. However, a month earlier, Khyber Pakhtunkhwa was the location of Pakistani strikes against its own civilians. On Sept. 22, an explosion killed more than two dozen people in the Tirah Valley region of the province. Police initially blamed the Tehreek-e-Taliban Pakistan (TTP), stating that bombmaking material had exploded in a compound in a remote part of the province. Others, however, were quick to attribute blame not to the TTP but to the military, which allegedly carried out air raids against militants in the borderlands with Afghanistan. If true, the implications of these allegations are severe, with Pakistani security forces responsible for killing their own civilians in two separate regions concurrently.

The issue is gaining further traction thanks to the local politicians in the province. The local member of the National Assembly for Tirah, Iqbal Afridi, has openly blamed the military for the airstrikes, as has Provincial Assembly member Sohail Khan Afridi. Both politicians are members of Imran Khan’s Pakistan Tehreek-e-Insaf (PTI), which governs the province. Considering Khan’s own grievances with both the central government and the military, it is unsurprising that members of his party are choosing to emphasise the military’s complicity in this tragedy. Unsurprisingly, in the aftermath of the strikes and the blame directed at the military, protests erupted in the province, with yet another government delegation required to negotiate with those involved.

Taken together, the crises unfolding across Gilgit Baltistan, Pakistan-administered Kashmir, and Khyber Pakhtunkhwa reflect deeper, fundamental problems at the heart of the current Pakistani state. Islamabad’s attempts to centralize control, whether driven by financial necessity or by rising militancy, have only served to intensify regional grievances and erode public trust. Now, as the dust settles on deadly clashes between Pakistan and Afghanistan, Islamabad’s most pressing challenge may not lie with its neighbors but within its own borders.