The suspects, aged 32 and 34, are accused of "belonging to and supporting an international terrorist organisation" and are also under investigation by Iraqi authorities, they said in a statement.
They are not believed to have committed any crime in Portugal.
Both men "were part of an Islamic State militia in Iraq" and were accommodated in Portugal in 2017 after a spell in Greece as part of a refugee programme, a police source told AFP.
IS, which controlled large swathes of Iraqi territory between 2014 and 2017, was officially defeated by government troops backed by a US-led international anti-jihadist coalition.
But cells of the organisation are still present in the country, especially in mountainous and desert areas, and claim occasional attacks.
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