The deportation came hours after a court held top officials in contempt for failing to release him from the airport where he was being held.
Kenyan officials have argued the lawyer - who holds dual Canadian nationality - is not a citizen.
But Mr Miguna, who was flown to Dubai, says their motives are political.
He has now appealed for help through his social media accounts.
"I was dragged, assaulted, drugged and forcefully flown to Dubai," Mr Miguna wrote in a Facebook post on Thursday.
"I woke up in Dubai and the despots are here insisting that I must travel on to London."
He added he was being threatened, and wanted to fly to Nairobi and "nowhere else".
"I'm sick. My ribs and body is hurting all over. This is a travesty of justice," he wrote.
The interior ministry is expected to release a statement shortly, news agency Reuters reported.
The vocal opposition figure was first deported in February after taking part in the mock inauguration of opposition leader Raila Odinga as the "people's president".
He disputes President Uhuru Kenyatta's victory in last year's election.
Authorities said Mr Miguna only held Canadian citizenship, and took away his Kenyan passport.
He tried to re-enter the country on Monday, but was held in Jomo Kenyatta Airport in Nairobi after trying to gain entry with his Kenyan ID card.
Footage of security guards manhandling Mr Miguna as they tried to force him onto a plane the same day went viral, while a number of journalists covering the story were allegedly assaulted.
Mr Miguna told the BBC's Focus on Africa earlier on Wednesday that he was being held in a toilet, and his family had been denied access to see him. This, along with his other allegations, were denied by an MP from the governing Jubilee Party.
"I am telling the world nobody should believe anything which comes from Miguna Miguna - he is a man who will make all manner of allegations," Kimani Ichung'wah, told the BBC's Newsday.
On Wednesday, Kenyan High Court judge George Odunga said the country's interior minister, the head of police and head of immigration would be in contempt of court if they failed to release him from custody.
There are now questions about how the promised reconciliation between Mr Odinga and President Kenyatta will continue.
Earlier this month the two political leaders appeared in a surprise television address together, in which they promised to begin the process following last year's bitter vote and aftermath.
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