Brathwaite has made a decision to skip the three-match series, starting on Sunday in Karachi, while ODI skipper Jason Holder, Shai Hope and Ashley Nurse will also miss out.
The Pakistan Cricket Board have put in place stringent security arrangements for the West Indies team, with 8,000 policemen and paramilitary personnel guarding the visitors in and around the hotel and stadium.
The series of three back-to-back matches starts on Sunday.
Commenting on the tour, Cricket West Indies (CWI) Chief Executive Officer Jonny Grave said, "Following the successful hosting of the Pakistan Super League final in Karachi on the weekend, our squad are now en route to Pakistan for our three-match T20I series".
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However, following the successful staging of the ICC World XI series in Lahore last September, the ICC praised the PCB on security improvements, paving the way for future global tours.
"We have a very good squad, youngsters have done well in PSL and everyone has a chance to be in the final XI on match day", Mickey Arthur told media on the sidelines of the training session in Karachi. Pakistan captain Sarfraz Ahmed said he was overjoyed at the return of global matches to his home city.
"It is not fair to say that big West Indies players are not coming", Sethi told journalists at Karachi's Jinnah International Airport. "We expect the series to be highly competitive". "Just two of their players have refused to come to Pakistan due to their [prior] commitments in the Indian Premier League".
There has also been a recall to global cricket for wicketkeeper Denesh Ramdin, who last played in the shortest format for the Windies when they won the World T20 in 2016.
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Sarfraz said he hoped his team would keep the momentum.
The West Indies will take on Pakistan in a three-match Twenty20 series next month, but the men from the Caribbean will be missing a number of their top players.
Pakistan have included three newcomers in batsman Asif Ali, allrounder Hussain Talat and paceman Shaheen Shah Afridi - after the trio fared well in the PSL 2018.
Chairman of the CWI Selection Panel, Courtney Browne, said some of the players identified for selection, including regular T20I captain Carlos Brathwaite, had opted out of the tour due to security concerns.
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