The poll is the latest in a series of surveys that show plummeting support for Musharraf, who seized power as head of the military in a coup in 1999.
Parliamentary elections will be held in Pakistan on Monday.
According to the survey, 64 per cent said stability would improve if Musharraf resigned and 49 per cent say his re-election was invalid.
Musharraf's second five-year term as president was approved in November by the supreme court, but only after the president sacked the chief justice and other outspoken judges under a state of emergency.
The Pakistani president's approval rating was at 15 per cent, with three-quarters of the survey's respondents saying they would like him to resign.
Meanwhile, 44 per cent said they were confident elections will be free and fair, and 51 per cent were optimistic conditions will improve over the next six months.
The killing of Benazir Bhutto, a former prime minister, in December has created a wave of sympathy for the opposition, according to the poll.
Although a recent investigation by British detectives supported the government's version of events surrounding her assassination, suspicions and conspiracy theories have persisted.
When the team carrying out the BBC-commissioned poll asked people who they thought was responsible for her death, almost 40 per cent referenced the Pakistani security agencies or people linked to them.
The survey was conducted before the release of the British findings.