Sports minister Kumaratunga sacked Sri Lanka Cricket's governing body in March amid allegations of financial irregularities and appointed an interim committee to oversee the game.
Sri Lanka Cricket is incorporated as a private company but it is also registered with the sports ministry so that it can represent the country at international events.
Judges ordered Wednesday that an interim committee appointed in March by sports minister Jeevan Kumaratunga should control the cricket offices until the legal case over alleged financial irregularities is resolved.
An appeal by cricket chief Thilanga Sumathipala at the suspension of Sri Lanka Cricket would be heard on June 9, the court said.
Armed police on Tuesday seized the cricket headquarters in downtown Colombo to install government nominees and the court order effectively gives them legal control over the premises and staff.
Sumathipala had sealed the offices last month and sent the staff on paid leave.
The International Cricket Council last week recognised the interim committee after seeking legal advice.