Dr Lee becomes the second former Conservative GP/MP to join the Lib Dems this month - following health select committee chair Dr Sarah Wollaston's decision to join the party after the collapse of the breakaway Change UK party.
Dr Lee hit out at the government and the current Conservative leadership in a strongly worded statement outlining his decision to defect.
The Bracknell MP, who continues to work as a GP, said: 'This Conservative government is aggressively pursuing a damaging Brexit in unprincipled ways. It is putting lives and livelihoods at risk unnecessarily and it is wantonly endangering the integrity of the United Kingdom.
'More widely, it is undermining our country’s economy, democracy and role in the world. It is using political manipulation, bullying and lies. And it is doing these things in a deliberate and considered way.'
After a great deal of thought, I have reached the conclusion that it is no longer possible to serve my constituents’ and country’s best interests as a Conservative Member of Parliament. My letter to the Prime Minister: pic.twitter.com/0QreSbSdwR— Dr Phillip Lee MP (@DrPhillipLeeMP) September 3, 2019
Dr Lee's decision to quit the party leaves the Conservative government one short of a majority despite the support of the DUP - and takes the total number of Lib Dem MPs to 15.
A former junior government minister, Dr Lee resigned from his role as a parliamentary under secretary of state at the Ministry of Justice in 2018 over Theresa May's government's handling of Brexit.