Safety experts are wading through the backlog of safety checks to homes after the Vltava River burst its banks, causing devastation in the city.
In the worst-hit area of the city, Karlin, up to 10,000 people are facing a delay of at least another fortnight before their homes can be declared safe.
Some buildings have been rendered permanently uninhabitable.
On Tuesday, thousands of Karlin residents were given the all-clear to return home, when the authorities reopened parts of the suburbs.
But the thousands of others remain in emergency accommodation or camped out with relatives.
Emergency workers were continuing to check for possible hazards, said city hall spokesman Martin Kupka.
At least three blocks of flats collapsed in Karlin, and some 40 other buildings have been declared dangerous.
Disease threat
Experts fear some areas may remain uninhabitable.
Even some of those who have been told their homes are safe still cannot return, as they have no electricity or gas supplies.
Prague resident Julie Ronkova told Czech online newspaper Pravo: "It's desperate. We don't have electricity or gas - only cold water. How can you live in a place like this."
She says that after three weeks of camping out with relatives, she now has nowhere left to go.
Officials say up to 5,000 new homes will be needed across the Czech Republic. Damage is estimated at 90 billion koruna ($2.9bn).
As the clean-up continues, the first three cases of the flood-related disease leptospirosis, or Weil's disease, were recorded in the south of the country.