Jenson Button was stripped of his third place at last month's San Marino Grand Prix and BAR were suspended for breaking the rules on their car's weight and fuel tank.
"We feel the FIA ruling is too severe," Honda spokesman Tatsuya Iida said on Monday.
"We gave them proof we didn't break the rules. To be accused of cheating was hurtful."
Honda, who supply BAR's engines, complained that Formula One's governing body FIA should have made the rules clearer to begin with.
"We have also kept to the rules. The regulations are very ambiguous," said Iida. "There should be a clear definition. We don't understand the punishment."
FIA appealed against the decision of stewards not to take action over the weight of Button's car at Imola and called for BAR to be banned for the rest of the championship.
An appeal court finding last week spoke of a "special compartment within the fuel tank" but Honda argue that FIA had known about modifications to the BAR car.
"FIA knew we had a new device in the gasoline tank," said Iida. "Without it the car won't move. We feel we didn't break any rules and the stewards agreed so it's very sad."
Button and Japanese team mate Takuma Sato will also miss the Monaco Grand Prix on May 22 after a six-month ban to come into effect after that race was suspended for a year.
The FIA ban was the harshest action taken against a Formula One team for 20 years. BAR team boss Nick Fry said he was "appalled" by the punishment.
"We struggled at the start of the year with the new car and just when things had started to come right, this happens," said Iida. "It's a terrible setback.
"It's not about the financial implications. We're not thinking about that. The decision is simply bad for the sport."
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