"The amnesty is intended to allow those who fought the government directly or indirectly to come out and participate in the reconciliation process," Justice Minister Hassan Dhimbil Warsame told IRIN on 19 June.
The pardon was announced in a presidential decree on 18 June. "The aim is to reduce lingering animosity caused by the fighting between the insurgents and Ethiopian-backed government forces," the minister added.
The decision, which follows the postponement of the national reconciliation conference from 14 June to 15 July, does not cover those who "engage in international terrorism", he added.
"The government has already started releasing people, who were detained on suspicion of involvement in the fighting," Warsame said. "As of last night [18 June] people have been released and we will continue to release more."
The Special Representative of the UN Secretary-General to Somalia, François Fall, welcomed the amnesty, saying it was "a good decision and a step in the right direction".
However, he said, the government needed to take it further and allow more people to participate in the reconciliation process that will culminate in the national conference due to be held in the capital of Mogadishu.
A regional analyst, who requested anonymity, told IRIN the amnesty might go some way to respond to demands by Hawiye clan elders for a secure venue and safety for those who will attend.
Haji Abdi Iman, the chairman of the Hawiye Elders' Council, recently told IRIN the conference should be held at a neutral venue, where people would be free to express their views.
"This is a sign of a little give and take but more is needed," the analyst said.
A civil society source in Mogadishu said the decision was welcome, but it needed to be followed by the lifting of martial law and a cessation of hostilities.
"Releasing individuals without dealing with the causes that brought that [the hostilities] about is meaningless," the source said. "If hostilities continue and martial law is still in place they can easily be rearrested. It will take much more to convince people that the government is serious about reconciliation."
Despite the announcement, violence continued in Mogadishu, where displaced people are trickling back, forcing some of the returnees to head off again. A civil society source said the displaced were going both ways - some coming while others were leaving.
On 18 June, a remote-controlled device was detonated in the north of the city, close to the proposed venue of the reconciliation conference, as a convoy of government vehicles passed by.
Two children who were playing in the vicinity were killed and seven others were injured, a local journalist said. The same day, presidential spokesman Hussein Mohamed Mahamud was shot twice by a gunman near the Bakara market.