Kenyatta won a second five-year term in office during the rerun, and he was sworn in as the country's leader in a ceremony last November.
Kenyan authorities have lifted the ban on NTV and KTN which can now be accessible on air after a ban on four TV stations for attempting to broadcast the mock inauguration of opposition leader Raila Odinga.
Two other opposition lawmakers were also arrested and later released for their involvement in the ceremony.
Miguna's arrest has sparked protests.
He was released on a $500 bail but has remained in police custody with his whereabouts unknown.
High Court Judge Luka Kimaru stated that police, in detaining Miguna, were operating outside the constitution and the law.
In the first charge Miguna is accused of being present and consenting to the administration of an oath to commit a capital offence namely treason contrary to section 59 (a) of the Penal Code.
National Super Alliance (NASA) lawyers who had assembled at Milimani Courts ahead of Miguna's hearing said the move by DCI only makes matters worse.
The government has ignored a court order issued on Thursday that the stations be allowed to reopen.
The government suspended the passports of 14 opposition leaders including strategist David Ndii and financier Maina Wanjigi.
Odinga's supporters protested against the charges, blocking roads and clashing with police in the western city of Kisumu, a Reuters witness said. A government official, who asked not to be named, confirmed its authenticity. Mr Odinga boycotted a re-run election in October, saying no reforms had been made to the electoral commission.
The free-to-watch channels which were shut down are still not back on air.Furthermore, the opposition claims their MPs and prominent voices are being arrested and held "incommunicado."The Kenyan government has so far declined to comment about the TV station shutdown despite numerous requests from CNN".
The Committee to Protect Journalists (CPJ) said government's refusal to abide by court orders was contempt for the rule of law and a brazen example of censorship.