A spokesman added that the players had no safety fears about returning home, although he admitted that Pakistani cricket fans would be disappointed with their performance.
"I would say that the Pakistani team was never a suspect. We had nothing to do with it," Pervez Mir said outside the team's hotel near London Heathrow Airport, where the squad has been staying since arriving from Jamaica on Sunday.
"We were part of the same inquiry as everybody else so of course we were questioned," he added, saying that Jamaican police had confirmed they were "not suspects."
Captain Inzamam ul-Haq made no comment as he left the hotel, along with other squad members. A group of eight or nine players had already left during the day, and more were to follow during the evening.
The Pakistan team arrived in London on Sunday for a pre-arranged stopover en route home after their trip to the Caribbean.
The players, said to be devastated at Woolmer's death hours after they were dumped out of the Cricket World Cup by minnows Ireland, have made little or no comment during their London stay.
Their planned departure came as a British press report said Jamaican police were searching for three of the Pakistan team's fans who spent a great deal of time with the players, in order to "eliminate them" from enquiries.
The three reportedly were close to the players and appeared with them at press conferences and after matches. The paper said they are believed to have left Jamaica shortly after Woolmer was found dead on March 18.
The spokesman said the report was a "joke," adding that the three identified men were well known to the team.
Woolmer, 58, was found unconscious in his hotel room, and declared dead hours later.
His mysterious murder came just one day after the shock defeat to debutants Ireland, stirring speculation that match-fixing gangs may have been involved in the murder.
In a separate interview with Sky News television, Mir conceded that Pakistanis would feel let down by their team's performance in the Caribbean.
"I'm sure the people in Pakistan are disappointed, and rightly so," he said, adding: "The players themselves are disappointed for underperforming."
Dismissing security concerns, Mir said: "There are always certain people who are a little over the top," he said, while voicing confidence that Pakistani authorities had taken sufficient precautions.
"We don't have to worry about that," he said, adding: "There is no concern, particularly when you go back to your home country."
The spokesman also rejected reports of a major split between Woolmer and members of the team, including the captain.
"There were a lot of rumours that I had rowed with Inzamam and that was a joke. But at least I was here, thank God, to answer those questions. Mr Woolmer is not here," he said.
"He was a very good man, a good coach and a father figure. Let's remember him for all those things rather than tarnish his memory."