According to the Czechpoint101 portal in Q4 2016 the prices for the apartments and flats are still going up.
For example, prices for apartments in Q4 grew by 3.9%, as for the whole year the grows was 11%. Apartment and flat prices climbed 3.9% in Q4 2016 meaning the year-over-year reached 11%.

Petr Němeček, director of Hypoteční banka, declares: “Nationwide price the growth was driven primarily by apartments in Prague, Brno, Olomouc and in the region around Prague, where housing prices also increased. It is worth noting that the prices of older prefabricated dwellings grew more than brick. The market is growing mainly among those interested in apartments for families (3 bedrooms, 3 + 1). This interest peaked in the last quarter, as sales of apartments in new buildings. A large part of new housing is bought purely for investment. In Prague, it is estimated to be up to 30%.”