The UK Border Agency (UKBA) may be unlawfully discriminating against Pakistanis, the man appointed to scrutinise the organisation has said.
Independent chief inspector John Vine said it was harder to enter the UK from Pakistan than from Bahrain, Abu Dhabi and Dubai.
He said staff applied higher evidential requirements for entry and made worryingly inconsistent visa decisions.
The government said the process was designed to target visa fraud.
Pakistan is the fourth largest source of applications to enter the UK.
Mr Vine, who was appointed by the government in 2008 to act as the UKBA's watchdog, said there was a worrying lack of confidence in the work of the visa section - particularly in Pakistan visa operations.
He said senior managers were dismissive of appeal decisions and staff applied "higher evidential requirements for entry to the UK to customers from Pakistan, and this was not made clear to them".
Mr Vine said: "I believe this means that the UK Border Agency was not only failing to be open and transparent about their approach towards customers, but also may be discriminating unlawfully in favour of Gulf Co-operation Council customers and against Pakistanis."
The Gulf Co-operation Council includes Abu Dhabi, Bahrain and Dubai.
Mr Vine added: "I believe the UK Border Agency must take immediate action to ensure it is acting in compliance with its duties under the Race Relations Act 1976."
Pakistan has seen major changes to its visa operation, partly as a reaction to its deteriorating security situation.
Immigration Minister Damian Green said: "Our tough checks are there not to target genuine applicants but those who try to obtain a visa through fraudulent means.
"That is why we will continue to work closely with the government of Pakistan to stamp out any abuse, and why we take a risk-based approach to decision-making, giving extra scrutiny to those countries where historically fraud has been higher."
He said "numerous improvements" had been made since the inspection was completed in May, and that 95% of visa applications were now processed within 15 days.
Mr Green added that a priority service for the Pakistan business sector has a turnaround time of three to five days.