Both were detained by police in the early hours of Monday after arrest warrants were issued at the weekend.
Nuriye Gulmen and Semih Ozakca were sacked under the state of emergency imposed after the July 15 attempted coup seeking to overthrow President Recep Tayyip Erdogan that has seen tens of thousands lose their jobs.
Former primary school teacher Ozakca and academic Gulmen began their hunger strike 75 days ago and have been surviving on water alone.
Both were detained by police in the early hours of Monday after arrest warrants were issued at the weekend, NTV broadcaster reported. The charges were not made clear.
Their lawyers and Ozakca's wife Esra tried to stop officers detaining the two but found themselves also taken into custody, NTV said.
Gulmen said on Twitter that police from the "political department were trying to enter the house. They are breaking the door at this moment".
"Damn fascism! Long live our hunger strike resistance! We want our jobs back! We have not surrendered and we will not surrender!"
Ozakca also wrote on Twitter around 1:00 am (2200 GMT) saying: "Our home is being raided".
Recent images of them showed their declining health and weight loss as they continued to hold demonstrations begun nearly 200 days ago by a statue celebrating human rights.
Necati Yilmaz, a lawmaker from the main opposition Republican People's Party (CHP), said on Twitter they were detained because of the risk "their protest would become a death fast and spark new Gezi protests".
He was referring to the protests in early summer 2013 against the planned redevelopment of Gezi Park in Istanbul that snowballed into national demonstrations against Erdogan's Islamic-rooted government.
Over 100,000 people from the public sector including judges, teachers, doctors and members of the armed forces have been dismissed in a series of purges criticised by the West and human rights activists.
Amnesty International criticised the "arbitrary dismissals" in a report released Monday, calling on the Turkish government to set up a "prompt and effective appeal mechanism" for those dismissed.