Misbah is currently struggling with poor form with the bat and pulled out of the third and final one-day against Australia in Abu Dhabi on Sunday.
Federal Bureau of Revenue (FBR) spokesman Shahid Hussain told media that batsman Azhar Ali’s accounts have also been frozen.
Hussain said: “Misbah has not paid taxes of 3.9 million rupees and Ali owes 1.5 million rupees in taxes, so the FBR has frozen their accounts and as per rules, their banks will be asked to deduct the amount if it is there in their accounts.”
A number of players have been investigated for tax evasion of the past few years.
In 2012, the FBR warned Misbah and a number of players over tax evasion, and in July this year the 40-year-old approached finance minister Ishaq Dar to resolve the income tax issues.
Dar reportedly promised to resolve the issue but categorically told the players that paying taxes is a national obligation for every citizen.
Tax evasion is rampant in Pakistan -according to FBR figures, less than 0.5 per cent of Pakistanis pay income tax, or just 750,000 individuals out of a population of some 180 million.
Misbah told AFP on Monday that he will only play one-day internationals if his form returns and will not allow the team to suffer because of his poor batting, which saw him score just 82 runs in the last five one-day innings.
Pakistan Cricket Board chairman Shaharyar Khan Sunday said it will be Misbah’s decision to lead or leave the one-day captaincy but his board was firm on retaining him until next year’s World Cup, to be held in Australia and New Zealand.