"We will ask for three replacements," Pakistan team manager Yawar Saeed told reporters ahead of a warm-up match against Somerset Thursday.
The three players, who were attending a meeting at the Pakistan High Commission in London, have been accused of taking bribes to fix incidents during the Lord's test against England last week.
"The T20 squad will remain as it is, this means 13 people," added Saeed. "For the 50-overs matches, we will be asking for replacements to make up the squad of 16 again ... we are today 13 and we will get another three to make it 16."
Pakistan have two Twenty20 games in Cardiff followed by five one-day internationals against England.
The three players implicated in the scandal had to wade through a media scrum on their arrival at the High Commission in London, with Butt refusing to answer shouted questions.
England and Wales Cricket Board chairman Giles Clarke, who also chairs the International Cricket Council's Pakistan Task Team, welcomed the Pakistan decision in a statement read to reporters.
"We look forward to an extremely competitive series, full of excellent cricket," he said.
"We can assure the fans across the country that the matches will be played in the most competitive spirit long associated with contests between England and Pakistan."
(Additional reporting by Alan Baldwin, editing by Jon Bramley)
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