"Law and order officials, having arrested a suspect, do not always inform the local authorities and the families of the detained, which is a breach of the law," President Alu Alkhanov was quoted as saying by Itar-Tass news agency on Tuesday.
Between 3000 and 4000 civilians have disappeared in Chechnya since hostilities resumed in 1999 between Russian federal forces and separatists, according to estimates by non-governmental organisations.
Rights groups say Russian troops and Chechnya's pro-Moscow authorities are responsible for the vast majority of the disappearances.
Some victims have been released, others have been found dead and yet others remain missing.
However, Alkhanov, whose predecessor Akhmad Kadyrov was killed in an attack in May, insisted that the situation in Chechnya was "improving".
He quoted official figures saying that 175 people had been reported missing since the start of 2004, half the figure for 2003.
Russian troops are accused of
numerous human rights abuses
However, the figures compiled by non-governmental organisations in Chechnya are much higher, with nearly 300 civilians reported kidnapped this year, according to the respected Russian human rights group Memorial.
Alkhanov also said a number of people reported missing were in reality separatist fighters whose families sought to disown them.
"It happens that a person takes to the forest [to join the separatist ranks] and that his relatives, to hide the fact that one of their own is part of an armed group, tell the police that he has 'disappeared'," he said.
The president also charged that a number of "criminals" were "transformed" into missing persons in the process.
International bodies have often criticised Russia for human rights abuses during the second Chechen war, which started in October 1999 when Moscow poured troops into the rebellious republic.