Lord Drayson is responsible for science policy across government
A minister has said the removal of the government's chief drugs adviser in a row over cannabis was a "big mistake".
In a leaked e-mail published by The Sun, science minister Lord Drayson said he had been "pretty appalled" by the decision to sack Professor David Nutt.
Home Secretary Alan Johnson said Prof Nutt "crossed the line" in his role by campaigning against government policy.
And Gordon Brown defended his removal, saying the government could not afford to send "mixed messages" on drug use.
Prof Nutt was controversially axed from his unpaid role as chairman of the Advisory Council on the Misuse of Drugs after using a lecture to say that cannabis was less harmful than alcohol and tobacco.
He also said it had been upgraded from class C to class B - against the council's advice - for political reasons.
The fallout from the decision continues to reverberate around Whitehall and the scientific community.
E-mails printed by The Sun appeared to suggest Lord Drayson was concerned about Mr Johnson's decision.
The newspaper reported him as writing: "Alan [Johnson] did this without letting me know and giving me a chance to persuade him it is a big mistake.
"Is Gordon [Brown] able to get Alan to undo this?" the e-mail reportedly continued. "As 'science champion in government', I can't just stand aside on this one."
Lord Drayson, a former businessman, is responsible for science policy within the Department for Business, including relationships with research councils and the interaction between science and society.
In a later statement, Lord Drayson said he had not been fully appraised of the situation when sending the e-mail in question.
He added that he had since spoken to the home secretary and received assurances about the important role that scientific advice would continue to play in informing government policy.
Prof Nutt has attacked the decision to remove him, saying it gave the impression ministers could treat advisers they disagreed with like "serfs".
Two other panel members have quit in protest at Prof Nutt's exit, saying it threatens to compromise the body's independence, while other members have sought a meeting with Mr Johnson to discuss the body's future.
And the government's chief scientific adviser has said he agrees with the basis of Prof Nutt's arguments over the relative harm of cannabis.
"I think the scientific evidence is absolutely clear cut," Professor John Beddington told the BBC. "I would agree with it."
Prof Beddington said he recognised there had been a breakdown in trust between Prof Nutt and the home secretary and therefore it was "difficult" for him remain in the role.
But he added: "I think it is fair to say we need to make a distinction between scientific advice and evidence - which is the role of experts and scientific committees - and the role of ministers, which is to make policy."
Mr Johnson told MPs on Monday he had asked Prof Nutt to step down because he had failed to distinguish between providing advice and criticising settled policy.
In his first public comments about the row, Gordon Brown strongly backed the decision, saying Prof Nutt had repeatedly undermined Labour's drug message.
"I think Alan Johnson made the right decision because we cannot send mixed messages," he said.
"Scientific advice is very important and we value it. But advisers advise and ministers have to make decisions.
"In the interests of the public we have to show we are tough on drug dealing and the problems that drugs are causing in our communities.
"We cannot send out a message to young people that it is OK to experiment with drugs and to move onto hard drugs. We have to send out a message to young people that it is simply not acceptable."
The Conservatives have supported Prof Nutt's dismissal but the Liberal Democrats say he did not breach any code of practice.