A spokesman for Gov. Andrew Cuomo said Monday morning the administration is “surprised” Comptroller Tom DiNapoli will opt out of the public financing system included in the state budget.

The budget includes a public financing system, but it is only for the comptroller’s race this election cycle.

DiNapoli has supported a measure that would create a public financing program with a small-donor public matching system for his race in the past.

But his re-election campaign is choosing to opt out of the program, citing the measure’s differences with what was approved in the state budget.

Cuomo’s office doesn’t see much distinction, however, between DiNapoli’s proposal and what was finalized in the budget agreement.

“We are surprised that the Comptroller is opting out, as this was the Comptroller’s bill to begin with. If he has specific concerns, we will modify the proposal, unless, of course, he just doesn’t want to do public financing,” said Matt Wing.

Good-government groups and advocates for public financing have blamed Cuomo for not securing a statewide system of public financing and are supportive of DiNapoli’s move to opt out of the system.

Advocates for public financing have questioned whether the Board of Elections is suited to develop a public financing system in the middle of an election cycle.

Nevertheless, the outcome in the budget has highlighted yet another sore spot between Cuomo and DiNapoli.

As a candidate in 2010, Cuomo did not endorse DiNapoli for a full, four-year term (that he did absolve him of wrongdoing in a pension-fund scandal his office was investigating).

Since the campaign, there has been little love lost between the two men, with each side using various auditing powers to release reports critical of their offices.