The two men, aged 27 and 31, were found guilty by a Swedish court in 2005 of raising money for the fundamentalist Islamic organisation Ansar al-Islam based in northern Iraq.
The men were sentenced to four and half years and five years in prison respectively.
Both were banned from returning to Sweden after serving their jail terms.
The pair were formally released earlier this year after serving two thirds of their terms including time prior to their trial.
While the Justice Ministry considers whether to deport the men, they are to remain in custody.
The decision on whether to release or continue to hold the men is renewable every two months, and in similar cases in the past, people have been held for up to two years.