Israeli Prisons Authority representative Sivan Weizman said Barghouti had been placed in isolation for a period of seven days following the publication of a letter last week "that called on Palestinians to take action against Israel."
The letter was considered incitement, she said.
In addition to the period of solitary confinement, Barghouti will not be allowed visitors for 30 days, she said.
Last week Barghouti released 17-point letter from prison outlining what he said was a new strategy aimed at achieving Palestinian statehood.
Among his suggestions, Barghouti called on the Palestinian Authority to halt its security coordination with Israel in the West Bank.
"The job of the Palestinian security services is to provide security and protection to Palestinian citizens, not to protect the occupation," Barghouti wrote.
He also called for the end of previous efforts by the West Bank government of Palestinian Authority President Mahmoud Abbas to engage in negotiations with Israel and expressed his support for a campaign of boycotts, divestment and sanctions against the Jewish state.
"It must be understood that there is no partner for peace in Israel when the settlements have doubled," Barghouti wrote. "It is the Palestinian people's right to oppose the occupation in all means, and the resistance must be focused on the 1967 territories."
Barghouti is serving five life sentences following his 2002 conviction in an Israeli court for murder and other charges related to his role in planning attacks on Israelis.
He is considered by many Palestinians to be the most important prisoner held by Israel and for some he is seen as the only possible political successor to Abbas.
Abbas has said he will not seek reelection.
Barghouti has been put in solitary confinement multiple times for public statements leaked from prison.
Barghouti is a member of the central committee of the Palestinian movement Fatah, and a member of the Palestinian Legislative Council.