The three, who include the head of the commission's vote counting operations Rodrigue Maite and two local officials, were placed in custody after some legislative votes failed to reach counting stations in the southern Boganda region, the body's spokesperson Rigobert Vondo said.
"At the level of counting (the votes)...some 20 (results from polling stations) have disappeared," he said, adding the commission is trying to verify the information.
Joined by telephone while he was in custody, Maite said the voting records had been transmitted to a counting station headed by an "expatriate expert".
"It was at this level that the records disappeared," he said.
On Monday, the electoral commission announced provisional results from last month's legislative elections with the exception of Boganda and Birao in the north.
The results, put the party of President Francois Bozize in the lead, were denounced as a "masquerade" by opposition parties.
With just over 66% of the vote according to official results, Bozize's KnK party appears on course to win an absolute majority in the National Assembly during the second round scheduled for March 20.