The blast occurred before midday and Ambassador Jamal al-Jamal's family was also at the two-storey residence in a northern suburb of the Czech capital. But no one else was hurt.
"There has been a detonation of a so-far unidentified explosive mixture," spokesperson Andrea Zoulova said.
"The ambassador was injured ... and taken to hospital with serious injuries. At the moment it is impossible to specify what kind of explosive it was. A search ... is under way at the moment," she said.
A Palestinian official, told Reuters from Ramallah, "This explosion happened at his house. He recently moved there. He was taken to hospital. An investigation is under way."
A second Palestinian source told Reuters, "He moved an old case with him to the new house from the old house. And when he opened it, the explosion happened."
There were no visible signs of damage to the house from the street, according to a Reuters reporter at the scene.
Police cordoned off part of the street and half dozen police vehicles, two firetrucks and two ambulances were there.
The Palestinian Foreign Ministry said it will send a delegation to Prague "to help with the investigation".
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