In a press statement on Tuesday, the agency indicated that paperwork to facilitate Dr Miguna's re-entry has been sent to Jomo Kenyatta International Airport where he is being held since Monday.
According to the lawyer, filling of the documents would also mean that Miguna is illegally in the country and likely to be a trap set by the government.
The rival politicians vowed to unify the country after elections past year in which about 100 people were killed, majority in clashes between opposition supporters and security forces.
On Tuesday, the Immigration Department reiterated that Miguna was not a Kenyan citizen and must, therefore, fill relevant documents to reclaim his lost citizenship.
NASA co-principal Moses Wetangula has hit out at the government over the attempt to re-deport National Resistance Movement (NRM) general Miguna Miguna that resulted in a nine-hour stand-off at JKIA on Monday.
From the videos shared online, there was another attempt forcing him to board a plane headed to Dubai - but this time around he did not leave the country.
Human rights official says Miguna Miguna should be allowed into the country, as Kenyan authorities want to deport the politician again despite court orders.
The High Court has ordered the government to release lawyer Miguna Miguna from detention at the Jomo Kenyatta International Airport.
However, the government through the department of immigration refuted the orders and had been today pushing Miguna Miguna to re-apply for his Kenyan citizenship.
"We have not denied him (entry), we just need him to follow the process like everybody else", Interior Ministry spokesman Mwenda Njoka told Reuters via phone.
He spent the night at the airport and his lawyers revealed that he had not eaten for 24 hours.
He said that the return of Miguna's passport was one condition for an enabling environment for political dialogue, but did not specify any new plans by the opposition.