Portugal denied Wednesday it was refusing visas to Iranians for "political" reasons, and insisted the measure was "temporary".
The move came against a background of mounting tension between Iran and the West after Tehran breached a limit for uranium enrichment set in a 2015 nuclear deal.
"This decision is not political," a foreign ministry spokesman told AFP Wednesday.
"It is not related to security conditions in Iran or any other aspect of an institutional or political nature," the ministry added in a statement.
On Tuesday, Foreign Minister Augusto Santos Silva announced a decision to suspend the issuing of visas to Iranians for "security reasons", telling parliament: "Portugal does not joke around with entries into its national territory."
The minister said he would not elaborate on the reasoning in public, though he later told local media the suspension had "nothing to do with the quality of bilateral relations between Portugal and Tehran."
Iran and the United States have been engaged in a war of words since Tehran in recent weeks enriched uranium past the limit set by a landmark 2015 nuclear in response to Washington pulling out last year.
There has also been tension on the high seas, after the British Royal Marines helped Gibraltar authorities detain an Iranian tanker that US officials believe was trying to deliver oil to Syria in violation of sanctions.
In response, Tehran has issued a series of increasingly ominous warnings to both the US and Britain about its right to take unspecified actions in reprisal.
And France has expressed concern about the fate of a French-Iranian academic arrested in Iran, the latest in a long list of dual nationals held in the country's prisons.