According to the newspaper, Ogundipe was arrested over a story on the report Ibrahim Idris, inspector-general of police (IGP), submitted to Acting President Yemi Osinbajo over the blockade of the national assembly.
Idris submitted the report after the sack of Lawal Daura, former director-general of the Department of State Services (DSS).
The IGP had requested that the force be given the permission to search the residences of all the suspects involved in the national assembly blockade, including Daura.
Irked by the leak of the story, the IGP was said to have ordered the arrest of Premium Times journalists.
Also arrested were Musikilu Mojeed, editor-in-chief of the newspaper, and Azeezat Adedigba, an education correspondent who was later released.
The newspaper said the police have been pressurising Ogundipe to disclose the source of the story.
It also reported that the police had placed a restriction on the bank account of Ogundipe.
The action of the police sparked an outrage on social media, with activists and civil society groups calling for his immediate release.
#FreeSamuelOgundipe is currently trending on social media