U.S. State Department Spokesman Sean McCormack announced that Pakistani officials had considered Musharraf's reason for skipping the meeting with U.S. and Afghan officials, though he added he would not elaborate on Pakistan government's explanation.
"President Musharraf certainly wouldn't stay back in Islamabad if he didn't believe he had good and compelling reasons to stay back," McCormack said. "Certainly we would understand that."
U.S. officials had earlier tried to persuade Musharraf to attend at least part of the council with hundreds of Pakistani and Afghan tribal leaders aimed at reining in militant violence now plaguing both countries.
Pakistan's Foreign Office said in a statement that Musharraf had phoned his Afghan counterpart Hamid Karzai on Wednesday to say he cannot attend because of "engagements" in Islamabad, and that Prime Minister Shaukat Aziz will take his place.
The Bush administration, which had brokered the meeting, was initially surprised by Musharraf's snub particularly after Karzai repeatedly expressed satisfaction about the meeting during a joint appearance with President George W. Bush on Monday.
The U.S. ambassador in Pakistan, Anne Patterson, has been in touch with Pakistani officials inquiring about Musharraf's cancellation.
The idea for the jirga was hatched in September 2006 during a meeting between Bush, Karzai and Musharraf in Washington as a way to stem rising cross-border violence.
The absence of Musharraf, Pakistan's army chief and most powerful figure, could further undermine the effectiveness of the "peace jirga" due to start in Kabul on Thursday with more than 600 tribal leaders attending.
The four days of talks are already being boycotted by delegates from Pakistan's restive South and North Waziristan regions amid fear of Taliban reprisals.