Pakistani troops fighting Islamist militants in the mountains of South Waziristan have picked up the trail of a leading al-Qaeda figure wanted in connection with the attacks on America on September 11, 2001.

The Times was shown yesterday the German passport of Said Bahaji, a close associate of the September 11 hijacker Mohammed Atta. The army said that it found the passport and other documents in a mud compound in the village of Shawangai.

The documents, which show that Bahaji, 34, has been in Pakistan since early September 2001, appear to provide the strongest evidence yet of a direct link between Pakistani militants and al-Qaeda’s high command.

The army said that the village, captured this week in the latest effort to drive out militants who have been extending their operations ever closer to the capital, Islamabad, served as al-Qaeda’s command base. The Times saw documents showing the recent presence of other European citizens.

The battle for Shawangai lasted several days. “They were ferocious fighters and we had to battle hard to capture the village,” Lieutenant-Colonel Inam Rashid, the commanding officer who led the assault, said. His men had killed some of the militants but many others had escaped. Bahaji’s fate was unknown.

Another officer said: “We do not know whether he was killed or fled.”

Bahaji, a German citizen born to a Moroccan father and German mother, briefly served with the German Army before coming into contact with al-Qaeda. He was part of the Hamburg cell, sharing an apartment in 2001 with Mohammed Atta and Ramzi bin al-Shibh, the alleged mastermind of the September 11 attacks.

The passport showed that Bahaji arrived in Karachi on September 4, 2001. A senior Pakistani investigator said that he was accompanied by Abdullah Husayni, a Belgian, and Ammar Moula, an Algerian with a French passport. Both were closely linked with al-Qaeda.

There was no indication that Bahaji ever left Pakistan. Pakistani investigators said that he stayed in Karachi in a hotel for several days where he was in contact with al-Qaeda members. He is believed to have moved to South Waziristan in 2002. The militants have been gathering strength in the region ever since.

Yesterday the mountains around Shawangai echoed to the sound of artillery fire as the army laid siege to the town of Kaniguram about 12 miles away. “It is going to be a tough fight but we will drive them out in the next few days,” Brigadier Ihsan Ullah said.

Kaniguram, with a population of 90,000 before the offensive, is considered a significant militant fortress. It sits at the centre of a network of roads leading to far-flung corners of the tribal region. Almost the entire population has fled. The town is under the control of the hardline Islamic Movement of Uzbekistan, whose leader, Tahir Yuldashev, was killed in a US drone attack last month.

Officers said that about 1,500 Uzbek fighters were entrenched in Kaniguram. “They would fight to the death,” Major-General Khalid Rabbani, the regional commander, said.

The capture of the town could clear the way for troops to advance towards Saragoha, another key militant base.

More than 30,000 Pakistani forces backed by F16 jets launched an offensive this month to flush out al-Qaeda and Taleban militants from their stronghold in South Waziristan after a series of terrorist attacks across the country.

The government troops have made significant advances, capturing key areas such as Kotkai, the home town of Hakimullah Mehsud, the leader of the Pakistani Taleban movement.

This is the army’s third campaign in South Waziristan. The last two in 2004 and 2007 ended in failure, forcing the authorities to sign a peace deal with the militants that analysts say turned the area into an al-Qaeda and Taleban base.

Officers have vowed that this time they will not stop until the region is cleared of the militants.

The fighting has forced about 200,000 people from the battle zone, creating a humanitarian crisis as civilians try to escape before the harsh winter. A US-based rights group warned of a “catastrophe” if aid was not allowed in to help civilians trapped in the area.

Human Rights Watch said in a statement yesterday that the Pakistani authorities should ensure that civilians who could not escape the fighting had access to basic necessities.

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