Ricard Gonzalez, 63, told AFP on Tuesday that he fled Egypt two weeks ago on the advice of Spanish authorities who told him he was facing "an imminent risk of being arrested".
"I asked about the nature of the threat, they didnt elaborate on that," he said in a telephone interview.
But Egypt's press and information office which accredits foreign correspondents said that Gonzalez, who wrote for the Spanish daily El Pais, gave no evidence of any alleged threat.
It said that instead Gonzalez "chose to leave" Egypt, where he had been working as a foreign correspondent since 2011.
More From This Section
The statement insisted Gonzalez was "free to practise his profession as a journalist with no constraints" throughout his stay in Egypt.
Gonzalez said the Egyptian embassy in Madrid had expressed reservations about El Pais's coverage of the country under President Abdel Fattah al-Sisi.
The group is banned in Egypt and designated a "terrorist" organisation.