Pakistani security forces arrested a "senior al-Qaida operative" in Karachi on Tuesday, signalling the first significant move against Osama bin Laden's network inside Pakistan since his death on 2 May.

Security agencies in the port city of Karachi apprehended Muhammad Ali Qasim Yaqub, alias Abu Suhaib al-Makki, a Yemeni said to have worked directly under the al-Qaida leadership along the Pakistan-Afghanistan border. The army described the arrest as a "major development in unravelling the al-Qaida network operating in the region", triggering speculation it may signal a wider heave against Bin Laden's top lieutenants. However, Makki's seniority in al-Qaida was not immediately known. In the past both the US and Pakistan have retrospectively attributed seniority to previously unknown al-Qaida militants.

Since Bin Laden's death the US has put pressure on Pakistan to crack down on militants believed to be sheltering in Pakistan, including Ayman al-Zawahiri, the Taliban leader Mullah Omar, and the leadership of Lashkar-e-Taiba, which carried out the 2008 Mumbai attacks.

Senator John Kerry, visiting Islamabad for the Obama administration, on Monday presented a list of demands to the Pakistani government, but refused to say what they were. US officials are frantically sorting through a treasure trove of intelligence captured from Bin Laden's house, including hundreds of computer disks. It was not immediately clear whether Makki's arrest came from Pakistani or US intelligence.

The arrest offered a glimmer of hope in another gloomy day for Pakistan-American relations. Earlier there was an exchange of fire between Nato and Pakistani forces along the Afghan border that injured two Pakistani soldiers.

Two Nato helicopters opened fire on a Pakistani military post in Datta Khel, in North Waziristan, after coming under fire. Pakistan's army condemned the incident as a "violation of Pakistan air space". Nato said the helicopters scrambled after a Nato base came under fire from the Pakistani side of the border.

Meanwhile, a new account of Bin Laden's last moments emerged that suggested the American soldiers who killed him discovered his weapons only after he was dead. The Associated Press account, based on interviews with senior US officials, casts fresh light on the Navy Seal raid, painting it as larger and more perilous than previously reported.

The account may give ammunition to critics who say Bin Laden's killing was unlawful, and it throws up questions about how Pakistan's air defences failed to stop the American incursion.

The US raiding party slipped into Pakistan early on 2 May in five helicopters – two stealth Black Hawks carrying 23 Navy Seals, an interpreter and a sniffer dog named Cairo, and three large Chinooks carrying a squad of 24 backup soldiers that landed in a remote mountain area north of Abbottabad.

The Black Hawks were equipped with special technology to muffle the tail rotor and engine noise, the AP reported.

Some experts have speculated they were also equipped with a special skin to fool Pakistani radars.