The BBC's Martin Plaut, who returned to DR Congo to follow up his initial investigation into the allegations, says they have managed to bring a measure of stability since they were first established by the UN in February 2000.
They have also helped disarm the warring factions, run democratic elections and assisted with reconstruction.
But an 18-month BBC investigation for Panorama has found evidence that:
- Pakistani peacekeepers in the eastern town of Mongbwalu were involved in the illegal trade in gold with the FNI militia, providing them with weapons to guard the perimeter of the mines
- Indian peacekeepers operating around the town of Goma had direct dealings with the militia responsible for the Rwandan genocide, now living in eastern DR Congo
- The Indians traded gold, bought drugs from the militias and flew a UN helicopter into the Virunga National Park, where they exchanged ammunition for ivory
The UN looked into the allegations concerning the Pakistani troops in 2007.
It concluded that one officer had been responsible for dealing in gold - allowing traders to use UN aircraft to fly into the town, putting them up at the UN base and taking them around the town.
But the UN decided that "in the absence of corroborative evidence" its investigators "could not substantiate the allegation" that Pakistani peacekeepers supplied weapons or ammunition to the militia.
It did, however, identify "an individual who seemed to have facilitated gold smuggling".
But returning to eastern DR Congo, the BBC spoke to several residents of the mining town of Mongbwalu, who said they had seen the FNI re-armed.
One former militant told our correspondent he had witnessed seven boxes of ammunition being brought from the UN camp to re-supply the FNI during a critical fire-fight.
Two FNI leaders known as "Kung-fu" and "Dragon", who have been jailed in the capital, Kinshasa, have stated publicly that they received help from the UN.
Pakistani peacekeepers have helped train the army in DR Congo
The BBC managed to get into the maximum security jail and both confirmed this.
Kung Fu, whose real name is General Mateso Ninga, said: "Yes, it's true, they did give us arms. They said it was for the security of the country. So they said to us that we would help them take care of the zone."
The FNI has been described by Human Rights Watch as "some of the most murderous individuals that operate in eastern Congo".
The ethnic Lendu militia was involved in the bitter clashes with their Hema rivals in the Ituri district.
UN insiders close to the investigation told the BBC they had been prevented from pursuing their inquiries for political reasons.
Our correspondent says that in short, the Pakistanis, who are the largest troop contributors to the UN in the world, were too valuable to alienate.
Pakistan has said it has no means of influencing the UN and that there is no evidence that its troops were involved in an illegal gold trade or re-armed militia, describing the allegations as baseless.
The Indian Army told Panorama that an investigation by the UN watchdog had revealed that all but one of the allegations were based on hearsay or had no credible evidence.
The special representative of the UN Secretary-General in DR Congo, Alan Doss, told the BBC that any effort to re-arm militias "would be a great concern to us".
The UN's Alan Doss responds to the allegations
"After all, we've lost lives fighting these militias - let's not forget that," he said.
Mr Doss dismissed the allegations of the militia leaders who said they had received weapons from UN troops based in the country.
"Militia leaders are militia leaders. They always have their interests," he said. "All I can say is that this investigation didn't confirm that."
Our correspondent says these are not the only allegations to have been brought against peacekeepers in DR Congo.
In December 2006, then UN Secretary General Kofi Annan said Moroccan troops had been involved in widespread sexual abuse.
Panorama: Mission Impossible is on BBC One, 2030 BST on Monday 28 April 2008
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