Witnesses reported that two missiles had bit the south side of the office building, starting a fire.
Israel has threatened to target Mr Haniya following the capture of an Israeli soldier by Palestinian militant groups last week.
In response, Israel has launched a vast military operation in the south of Gaza as part of a continuing effort to secure the release of the soldier, Corporal Gilad Shalit.
Palestinian medical sources said a member of the armed wing of the Palestinian movement Hamas was killed in an Israeli air strike in the northern Gaza Strip town of Jabaliya.