Swiss Transport Minister Moritz Leuenberger said officials also mishandled the aftermath of the crash.
He was speaking at a memorial mass at the crash site in Ueberlingen, in southern Germany.
Earlier, the Swiss President, Kaspar Villiger, called off plans to attend a separate memorial service in Russia amid concern that his presence could provoke outrage.
Wrong words
Mr Leuenberger told mourners at the Ueberlingen ceremony that Swiss officials had been wrong immediately to blame the Russian pilot.
"The confrontation with the terrible notion of being part of the cause of the death of 71 people led us into helpless initial reactions, to confused and confusing information, to lapses," he said.
"Not everyone of us found the right words."
Mr Leuenberger said Switzerland was ready to offer compensation.
"Your pain is our pain," he told mourners.
Mr Leuenberger said families had a right to have their questions answered.
Investigation
An investigation into the cause of the crash which occurred when a Russian charter jet collided with a cargo plane under guidance from Swiss air traffic control on 1 July.
The victims included 45 children from the Russian republic of Bashkortostan.
The Swiss air traffic control company, Skyguide, has admitted that its collision-warning system had been switched off for routine maintenance at the time and that one of the two air traffic controllers on duty had gone on a break.
The investigation has also revealed that Russian and European pilots follow different procedures when responding to the warnings from their on-board Traffic Control Avoidance System (TCAS).
European pilots are advised to follow their TCAS at all times, even if its warnings conflict with air traffic control orders.
But Russian pilots are trained to take account of both before deciding themselves.
It is believed the Russian pilot ignored TCAS warnings to climb and obeyed orders from air traffic control to dive - which put his plane on a collision course with a DHL Boeing whose pilot followed a "descend" instruction from his TCAS.
Not welcome
Swiss President Kaspar Villiger, for his part, cancelled his plans to attend the service in the capital of Bashkortostan, Ufa.
The president's office said officials had been warned by the Russians that "emotions have been running high since Thursday evening in Ufa, and the safety of a Swiss delegation there on Saturday would have been endangered".
But in Moscow, the Russian Foreign Ministry said the visit was being cancelled only because it could be clouded by outrage from grieving relatives.
Spokesman Alexander Yahovenko said: "The point is not that we cannot guarantee the safety of the Swiss president.
"The Bashkir authorities think that the ceremony will be very charged, full [of] serious emotional shocks."
This, he said, could have "a negative effect" on the Swiss president's stay.
Many of the relatives of those killed in the crash between the Bashkirian Airlines jet and the DHL Boeing have already visited Ueberlingen and there have also been emotional funerals in Ufa.