A senior Malagasy official on Thursday said the government would continue to pursue individuals responsible for political violence following disputed elections in 2001.
However, he denied that the authorities had singled out supporters of former president Didier Ratsiraka for prosecution.
On Tuesday a criminal court in the capital Antananarivo sentenced Emilson (in some parts of the country people have a single name), the former governor of the central province of Fianarantsoa and a close ally of Ratsiraka, to five years in prison for threatening state security.
Emilson was accused of orchestrating the blockade of roads leading into the capital to starve the then opposition stronghold of fuel. Factories closed down and thousands of jobs were lost as a result of the siege. Prices of basic foods rocketed and aid workers warned of a humanitarian crisis.
During the political stand-off between Ratsiraka and President Marc Ravalomanana, Fianarantsoa was the scene of sporadic clashes between supporters of the two opposing camps. Emilson was one of five provincial governors who supported the setting up of a rival capital in Tamatave, rejecting Ravalomanana's election victory.
In recent months several high-ranking pro-Ratsiraka officials have been tried and convicted for their part during the crisis. That has sparked concern among rights activists that Ravalomanana had embarked on a witch hunt to track down supporters of the old regime. Ravalomanana has since dismissed those claims, and reiterated his government's commitment to national reconciliation.
"Each individual is judged on a case by case basis. There is nothing untoward about this. Emilson was found guilty after much research proved that he was directly responsible for the setting up of the barricades which restricted the free flow of goods and people during the political crisis. There is no systematic programme to target Ratiraka's allies just because they may have supported him," presidential advisor Didier Rakotoarisoa told IRIN.
But in a report released in December last year, Amnesty International claimed hundreds of people had been arrested and detained for alleged crimes during the nine-months of political upheaval, most of whom were Ratsiraka sympathisers.
The report implicated the country's security forces and supporters on both sides for numerous human rights abuses, including acts of extra-judicial executions and torture. It also echoed concerns raised earlier by the National Reconciliation Committee (NRC) over the lack of transparency in several arrests in the provinces, as well as conditions in which detainees were being held. The NRC was established in August last year by the government to oversee the post-election crisis.
"The evidence so far supports the government's claims that is will give everybody a fair trial but certain questions persist. It is still not clear why all of the accused were brought from their provinces to be tried in Antananarivo," civil rights activist Madeleine Ramaholimihaso told IRIN.
"This immediately disadvantages the defendant who does not have access to potential witnesses. There were arguments that the courts in the capital were best equipped to deal with this issue but that is a bit disingenuous on the part of government," she added.
Amnesty's report also highlighted the conditions detainees were being held in, saying there was little consideration for their physical and psychological well-being.
The report estimated that between 400 and 500 people arrested during the unrest were still being held in custody in overcrowded prisons. The government puts the figure at 200.
"We are trying to speed up our investigations regarding the detainees. Already some have been released but we have to make sure that we are not releasing the wrong individuals. We are trying to ensure that we are doing a thorough investigation," Rakotoarisoa said.
Madagascar's political crisis began when Ravalomanana accused Ratsiraka of rigging presidential elections in December 2001, preventing him from claiming a first round election victory. The country's Supreme Court subsequently ruled in Ravalomanana's favour, and his military forces overran pro-Ratsiraka provinces.
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