The Libertines' former frontman, who once dated supermodel Kate Moss, was asked to leave The Cabin -- a $12,000-a-month centre in northern Chiang Mai -- after three weeks of treatment.
British press reports said Doherty had been thrown out for disruptive behaviour, claims denied by the centre which said he was simply not ready to complete the rehab course and was discharged on Tuesday.
"It is important to maintain the integrity of the treatment programme for the other clients to have a good chance of recovery," said Alastair Mordey, part of The Cabin's counselling team.
"Pete understands this and therefore the reasons behind why we have asked him to leave.
"Although our parting with Pete is amicable, we are of course disappointed to see him leave. We hope some of the things he has learnt here will help him in the future and look forward to the day when Pete decides to consider recovery again."
Doherty cancelled several high-profile gigs to enter The Cabin's renowned drug addiction courses, which include intensive therapy, meditation and outdoor activities such as white-water rafting.
The famously dishevelled songwriter, who has maintained a wide fan base despite being jailed several times in Britain for drug possession, has tried to kick his longstanding habit on numerous occasions.
In May the hell-raising 33-year-old appeared at the Cannes festival in his first film role -- as a debauched young man in 19th-century France.