"Attiya Radwan, Head of the Museums Sector, clarified that no Islamic artefacts have left the museum or have been transferred to the presidential palaces. All are accounted for and in the care and custody of the museum curators," the ministry said in a statement.
No artefacts for which the Egyptian state is responsible are held in any presidential palaces, according to the statement.
"Mohamded Abbas, the director of the Museum of Islamic Art, stressed that if any artefact is on loan to another museum or exhibition abroad, all legal and safety protocol is adhered to," it said.
Artefacts are only moved in special circumstances, having gained the approval of a permanent committee and an administrative board at the ministry.
Abbas rejected the claims of the artefacts' theft published by El Shorouk News earlier on Monday and said none left the museum during the refurbishment.
The museum hold 95,000 treasures with 2,400 on display.