The private letter, seen by the BBC, said the current plans of people waiting up to 12 weeks for a second dose - which Health Secretary Matt Hancock said is supported by data from an Israeli study - are "difficult to justify".
It said: "The absence of any international support for the UK's approach is a cause of deep concern and risks undermining public and the profession's trust in the vaccination programme."
Appearing alongside Boris Johnson at Friday’s Downing Street briefing, Professor Whitty defended the policy saying it would double the number of people receiving jabs.
He said extending the gap was a "public health decision" that would allow "many more people to be vaccinated much more quickly".
The UK initially planned to leave 21 days between the first and second doses of the Pfizer vaccine, which became the first in the country to be administered to vulnerable people after it was green-lighted in early December.
But officials moved to increase the gap between both parts of the Pfizer and Oxford-AstraZeneca vaccines to 12 weeks.
The Department of Health and Social Care said the decision to extend the wait followed a review of the data and was "in line with the recommendations of the UK's four chief medical officers".
In the letter, the BMA said it agreed the vaccine should be rolled out "as quickly as possible".
But it called for an urgent review of the UK’s strategy and said the gap between the first and second doses should be reduced.
The doctors' union said the UK approach "has become increasingly isolated internationally" and "is proving evermore difficult to justify".
"The absence of any international support for the UK's approach is a cause of deep concern and risks undermining public and the profession's trust in the vaccination programme," the letter says.
Appearing on BBC Breakfast, the chair of the BMA, Dr Chaand Nagpaul raised "growing concerns" that the vaccine could become less effective when doses are 12 weeks apart.
"Obviously the protection will not vanish after six weeks, but what we do not know is what level of protection will be offered [after that point]," he said.
"We should not be extrapolating data when we don't have it."
Communities Secretary later said the 12-week vaccine gap is based on ‘very clear’ advice.
Appearing on Sky News, he said: "The government’s following very clear advice by the MHRA, our own experts and from the four chief chief medical officers of all parts of the UK, and they said that ensuring that someone is vaccinated for the second jab within 12 weeks is fine, and that’s what we’re following.
“As a result of that, we’re ensuring that millions more people can get the first jab.”
Public Health England medical director Dr Yvonne Doyle also defended the decision to delay the second dose of the coronavirus vaccine to 12 weeks.
Dr Doyle said the decision had been taken on "public health and scientific advice".
"The more people that are protected against this virus, the less opportunity it has to get the upper hand. Protecting more people is the right thing to do," she told the BBC Radio 4 Today programme on Saturday.
"People will get their second dose. As supplies become available more people will be vaccinated.
"It is a reasonable scientific balance on the basis of both supply and also protecting the most people."