The 37 and 42-year-old men were ordered to remain in custody despite their denials of the allegations. The pair are being held on suspicion of preparing acts of terrorism.
The prosecutor explained that the application was made to have the men kept in custody as investigations are not yet complete. The court has stated that charges must be brought before April 10th.
"It is doubtful that we will be finished by April 10th," said prosecutor Ronnie Jacobsson to news agency TT.
A 100 people with connections to various Somali associations demonstrated outside the court. The demonstrators called for the release of the men who it is claimed are politicians.
"It is very unfortunate that the men have been held in custody as they are both politicians active with the Somali opposition. They are now political prisoners in Sweden," said Abdirisak Aden, vice-chairman of the Somali Association of Sweden.
Aden emphasized that one of the men is the secretary-general of the Alliance for the re-liberation of Somalia (ARS), a group claiming to seek a political solution to the chaos in the country.
"Our demonstration aims to display our anger over Swedish anti-terrorism legislation. Somalis living in Sweden and active in the opposition are used, with the help of the law, as guinea-pigs."
The men were arrested in Stockholm in February on suspicion of passing money on to groups in Somalia with the intention of financing terrorist crimes. They were arrested as part of coordinated operations between Norway and Sweden. Six people were originally held of which two in Sweden, and one in Norway, remain in custody.
Swedish Security Service Säpo suspect the men of having links to the Al-Shabaab organization in Somalia.
Al-Shabaab, which translates roughly as 'Youth', is an extreme breakaway faction of the Islamic courts in Somalia.
The group claimed responsibility for a bombing in early February in the coastal town of Bosasso in Somalia Puntland region. According to officials, 20 Ethiopian migrants and guest workers died in the attack, which also injured around 100 people.