The new rules require officers to identify themselves
Lieutenant General Vladimir Moltenskoi said that from now on officers involved in the so-called "special operations" have been ordered to identify themselves when entering homes.
But human rights groups remain deeply sceptical.
"We are increasing the responsibility of all officials so that people stop disappearing without a trace," General Moltenskoi said in a statement carried by ORT television.
Kremlin spokesman Sergei Yasterzhembsky said the new measures would bring about a significant improvement in the situation in Chechnya and would help stem accusations from human rights groups of widespread abuses against the civilian population.
Villages blocked
During security sweeps, federal troops block off whole villages to search for Chechen fighters.
The decree says troops must now invite a whole range of people to accompany them on operations: from the head of the local administration, to village elders and even clergymen.
All vehicles should be clearly marked, soldiers can no longer remain anonymous - and the names of all those detained must be reported to the local authorities.
Mr Yasterzhembsky described the decree as unprecedented and said the measures were a significant step towards stabilisation in the republic.
But the head of Human Rights Watch in Moscow, Deidrich Lohman, says much of this is laid down in Russian law already.
He says similar promises have been made before - and that the real problem is ensuring that these measures are implemented.
Mr Yasterzhembsky cited the cases of over 30 soldiers already prosecuted for violations in Chechnya since the war began.
But human rights groups say that is a tiny figure compared to the thousands of civilians who have been injured and the more than 100 who have disappeared without a trace during sweep operations this year alone.