The ministry had denied that Miguna was being held illegally this week and said he had failed to follow arrival procedures when he landed in Kenya.
He shared photos of himself and his swollen hand, as he lied in a hospital bed moments after arriving at the Dubai Airport.
Canadian-based lawyer Miguna Miguna has spoken for the first time after landing in Dubai where the Government of Kenya "forcefully" deported him.
According to Mr Miguna, security officers burst into the lavatory in which he had been locked for three days on Thursday morning, assaulted him and then injected him in multiple parts of his body with an unknown substance.
His lawyer Nelson Havi while talking to a local TV station, said his client could not walk or stand and had been taken ill at a hospital at the Dubai Airport.
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There was no immediate response from Kenyan authorities, though Kenya's immigration department retweeted a post calling on the public to ignore a rumor that Miguna had been sedated or drugged.
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, the BBC reports.
High court judge George Odunga said on Thursday both men had "conducted themselves in a most despicable manner not expected in this constitutional era" - an unprecedented rebuke of such senior figures. He did not order them jailed because even "if they can't obey the orders of this court with such impunity" he doubted that junior officials would act on warrants to arrest them.
But Mr. Miguna, who was flown to Dubai, said their motives are political. A court later ordered that Miguna's Kenyan passport be restored and that he be allowed to return.
The judge also ordered that National Super Alliance activist Mr Miguna Miguna be released from detention, at the Jomo Kenyatta International Airport, unconditionally.
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He has now appealed for help through his social media accounts. "I have not eaten". I want to take a flight only to Nairobi. "I have not been given access to my lawyers, family members and physicians".
Miguna Miguna, the self-declared "general" of Kenya's National Resistance Movement (NRM), has alleged that he was drugged before being deported to Dubai on Wednesday night.
Odinga's supporters insist Kenyatta fraudulently won Kenya's presidential election in August.
Odinga had argued that Kenyatta lacked legitimacy because his initial August 8 re-election victory was nullified by the Supreme Court over "irregularities and illegalities".
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