The commissioners later voted unanimously to keep a record of their vote on pay raises in the minutes, though the governor's veto technically deleted it. Their action did not overturn the veto.
At issue was the commission's March 14 vote to appropriate funds for a pay raise of up to 5 percent for its 12 management and 33 unionized employees, pending a collective bargaining agreement.
Some of the money would have come from the Pinelands Conservation Fund, which in part is used for land acquisition.
On Monday, Christie vetoed the appropriation - it was the first time a governor had overturned a Pinelands Commission vote - and denounced it in exceptionally harsh language.
In his letter, Christie said use of the Conservation Fund for raises was tantamount to "confiscation by the commission of public funds," and a "conscious disregard of the fiscal realities" of the state and commission.
Commission members on Friday rejected that charge, noting that a portion of Conservation Fund money has long been used for salaries.
"Confiscation of funds?" asked Commissioner Edward McGlinchey. "I don't confiscate funds."
The commission's 33 unionized employees have been without a contract since July 2011, according to a spokeswoman for the Communication Workers of America.
Jenelle Blackmon of CWA Local 1040 said Friday that commission employees earn an average of 36 percent less than their counterparts at similar state agencies, and said the union had accepted unpaid furloughs and slashed negotiated pay raises in the face of threatened layoffs.
She accused the state negotiators of "stall tactics," including months-long postponements of negotiating sessions, and said the local may file charges of failing to bargain in good faith if the sides do not work toward a settlement.
Nancy Wittenberg, executive director of the Pinelands Commission and former member of its negotiating team, was out of state and unavailable for comment, said commission spokesman Paul Leakan. Leakan said he was not authorized to comment.
Commissioners estimated that a 5 percent pay raise for all employees would have amounted to about $123,000 for one year. Blackmon said about $88,000 of that would go to unionized employees.
Several commissioners, including Lohbauer, said they were concerned that employees would look for jobs elsewhere if they were not better compensated.
"I'd love to work with the governor to give the staff the compensation they deserve," said Commissioner Edward Lloyd.
It was unclear where funding for any future pay raises would come from.
Commissioners spent about 10 minutes debating whether to send a written reply to the governor that "sets the record straight about the many inaccuracies in the letter."
They decided not to send such a rebuttal, however, for fear it might antagonize Christie's aides and escalate into a feud.
"I don't think it serves anyone going back and forth publicly," said Commissioner Robert Jackson.
They agreed instead to discuss their concerns in private with the governor's office.
On Tuesday, the directors of the Pinelands Preservation Alliance and the Sierra Club of New Jersey voiced concern that Christie's veto and stern letter were expression of his anger that the commission recently blocked a natural gas pipeline from running through a section of protected Pinelands forest. The Christie administration had strongly supported the pipeline.
A spokesman for Christie called the retaliation theory "disconnected from reality" and said the governor's veto was driven by a concern for fiscal responsibility.