Judge Tharwat Hammad said that judicial authorities had opened an investigation into accusations that Morsi and eight other senior leaders of the Muslim Brotherhood had defamed the judiciary.
He said all were banned from traveling.
A prosecutor also ordered the arrest of the Muslim Brotherhood's supreme guide, Mohammed Badie, and a top deputy, Khairat el-Shater, for allegedly ordering the killing of protesters outside the Brotherhood's headquarters Sunday, judicial sources said.
It wasn't known where the two men were.
The action was taken as a judge appointed to Egypt's constitutional court by Hosni Mubarak — the strongman leader ousted by the Arab Spring uprising — was sworn in as interim president Thursday.
A crackdown on the Muslim Brotherhood movement got underway in Egypt on Thursday with the arrest of several leading members following the military overthrow of Morsi.
A leading member of the Muslim Brotherhood warned that the ouster of Morsi, a member of the movement, could prompt some groups to resort to violence, although he said the Brotherhood wouldn't do so.
A coalition led by the Brotherhood called on Egyptians to mobilize peacefully in a "Friday of Rejection."
A military source also told Reuters: "We will continue to secure the places of protest with troops, and jets if necessary, to make sure the pro- and anti-Mursi demonstrators don't confront each other. We will let them demonstrate and go where they want."
The deposed president was under house arrest at the Republican Guard Club, and most members of presidential team had also been placed under house arrest, a Brotherhood spokesman said.