HRC team principal Livio Suppo said that, while he was sympathetic to Ducati's priorities, its switch undermined what he believes is the fundamental basis for the Open class's creation.
He also voiced his disgruntlement over the release of new and more sophisticated spec software just days before Ducati confirmed its direction change.
Andrea Dovizioso, now riding an Open-class Ducati, finished just six thousandths of a second down on Honda's Dani Pedrosa after the second day of tyre testing at Phillip Island on Tuesday.
"As Honda, the position is clear; we understand that Ducati is behind, so they are trying everything to recover," Suppo told the official MotoGP website.
"Sure the Open class rules allow them to work on the engine during the season; this is important for them, I understand.
"On the other side, we are not so happy that - just a few days before the announcement of Ducati going Open - there was the introduction from Magneti Marelli of new software, which is much more complicated that the standard one of the Open class.
"I think this is something we need to speak about.
"At the end of the day, if the Open class is with a factory bike, very sophisticated software, more fuel, more testing, more engines [over a season], it is not a cheaper class compared with the factory bikes.
"I think that was the aim of the rule: to create a cheaper class. So I think we need to think about it."
Asked whether the works Honda team could be tempted to trial an Open class entry - and therefore benefit from the lack of engine freeze, extra fuel allowance and an allowance of 12 engines per season - Suppo said resolving the principles of the newly-created class was his only priority.
"We need to understand - together with Dorna and the MSMA - if it was clear to everybody what the aim of this class was," he said.
"Our understanding, and I think it was the understanding of everybody, was a class that was cheaper than the factory bikes.
"With the interpretation of Ducati, it is not.
"It is just a question of sitting down together around the table to see what we want for the future.
"If we want a cheaper class, this [Open] is not it."