At the same time, Sanaa defended its "positive" cooperation in the so-called war on terror.
"The United States has been exerting pressure on Yemeni authorities to allow them to interrogate al-Ahdal directly, but this has been refused," a Yemeni official said on Saturday.
On Friday, Yemen confirmed that it had arrested Muhammad Hamdi al-Ahdal, alias Abu Issam al-Maki, on Tuesday.
The government believes al-Ahdal is the top figure in the country's branch of Usama bin Ladin's network.
The Interior Ministry said it nabbed Saudi-born al-Ahdal in a sting operation in Sanaa, after one of his associates was arrested in early November.
"Hedi Dalqam, an al-Qaida activist, was arrested at the start of November," the official said describing him as a "colleague" of al-Ahdal.
Authorities believe al-Ahdal replaced Ali Qaid Sunian al-Harithi, alias Abu Ali al-Harithi, after the former al-Qaida Yemeni chief was killed with five others in a November 2002 missile attack by the CIA.
However, London-based Saudi newspaper Al-Sharq al-Awsat said on Thursday that some US officials "doubt the truth of announcements made by Sanaa regarding anti-terror operations".
The paper added that "some US weapons sold to the Yemeni government were smuggled to Saudi terrorists".
Yemeni authorities slammed the "false" newspaper report aimed at misleading "world opinion over Yemen's serious and decisive position in fighting terror and undermining the growing relations between Yemen, Saudi Arabia and the United States".
"Yemen will not succumb to any form of blackmail irrespective of its nature and source," said an interior ministry official quoted by the official Saba news agency.
The US had said last week that it was in the process of "confirming" al-Ahdal's arrest, adding that he may have been involved in the October 2000 attack against the USS Cole in the Yemeni port of Aden.
As proof of Yemen's commitment to the US' "war on terror", the official said al-Ahdal's arrest was announced "four hours" after it took place on Tuesday.
He also said cooperation between Yemen and Saudi Arabia was on the rise, following the signing of an agreement between the two countries in June to boost security measures at the border to prevent arms smuggling and infiltration.