It urged him to relinquish his role as head of the army no later than the end of 2007 - something he is already due to do in any case. No further action has been taken.
"The group expressed its serious concern and regret that President Musharraf has not met his commitment to relinquish his role as chief of army staff by 31 December 2004," it said after a meeting of the Commonwealth Ministerial Action Group (CMAG).
"CMAG expects the two offices not to be combined in the same person beyond the end of the current presidential term in 2007 at the latest," the statement said.
The CMAG is the steering committee of the 53-member organisation of mainly former British colonies.
The meeting included senior ministers from Nigeria, the Bahamas, Lesotho, Malta, Tanzania, Sri Lanka, Canada, India, the United Kingdom and Samoa.
Pakistan was suspended from the Commonwealth in 1999 after Musharraf took power in a bloodless military coup.
Initially he was treated as a pariah, but his frontline role in the US-led "war on terror" after the 11 September 2001 attacks on the US aided his international rehabilitation.
The country was readmitted as a full Commonwealth member in May 2004 after Musharraf agreed to give up his military post by the end of last year.
The Commonwealth suspended
Pakistan after Musharraf's coup
Nigerian Foreign Minister Olu Adeniji said after the meeting the possibility of again suspending Pakistan had been considered but rejected because there had been no consensus.
The Pakistani parliament approved a law last November permitting Musharraf to keep the two roles beyond the end of 2004 - in effect legitimising the backsliding on his original promise.
In Islamabad, Information Minister Shaikh Rashid Ahmad declined to comment on the Commonwealth committee statement, but government officials pointed out Pakistan's constitution bars the president from holding dual offices beyond 2007.