In the midst of the unfolding food stamp scandal involving state employees, Gov. Dannel P. Malloy urged his commissioners to foster a culture that encourages employees to come forward with any information about fraud and abuse within state agencies.

“They need to understand that they have nothing to fear,” Malloy told his commissioners Thursday at their monthly Capitol meeting. “And it’s your obligation to make sure they understand that.”

Malloy reminded them that there is a whistleblower statute in place to protect state employees who come forward will be protected under it, but he also said he wants his administration to go well beyond that.

“Although I’m glad we have the statute, we need to go well beyond the confines of the statute. We need to create an environment, an environment in which all of our fellow state employees feel comfortable bringing their concerns to us as managers,” Malloy said.

But a budget implementer negotiated by the legislature’s Democratic-majority and the Malloy administration now gives the Auditors of Public Accounts greater discretion as to which whistleblower complaints they investigate.

The language was prompted by a 2009 Program Review and Investigations Committee investigation that found the number of the complaints doubled between 2002 and 2008, straining the staff in the auditors office.

Republican Auditor Robert Ward said Thursday that under the new language some of the complaints being made as whistlerblower complaints will now be handled through the grievance process, if it involves a member of a bargaining unit, or the Commission on Human Rights and Opportunities, if it involves retaliation.

“It was about setting priorities,” Ward said of the changes made.

He said some of the complaints the office received were not about the use of public money, but about relationships between the employees and the state agency management.

A union spokesman said they had their concerns about the language because it means a lot more complaints will be investigated by the state agency in which the employee making the complaint works.

“We’re certainly all in favor of a culture that promotes openness and transparency, which didn’t exist under former Governors Rell or Rowland,” Matt O’Connor, spokesman for CSEA/SEIU Local 2001, said Thursday. However, it’s not clear yet if the language included in the budget encourages or discourages the culture Malloy’s trying to create.

Malloy, whose already had a rough and tumble year with unionized state employees over their collective bargaining agreement, said he doesn’t think the consolidation of state government or those conversations will impact the open culture he’s trying to create.

“That backlog of open complaints, if it exists, existed under the regime, the management style, the management system of another administration,” Malloy said. “So in and of itself, the existence of doing things that way did not prove to be successful and we’ll continue going forward to modernize Connecticut’s government to make sure we’re doing more with less.”

He said what he’s hearing from state employees is an expression of frustration that existed long before he became governor.

“I think the people who work for the state of Connecticut are deeply disappointed, offended, outraged that some number of their fellow employees may have taken advantage of this program illegally,” Malloy said. “I haven’t heard a single union leader defend it.”

The state is currently reviewing the applications of the 800 state employees who applied for post-Irene food stamps. The 15 employees already referred to their respective commissioners for disciplinary action had income that far exceeded the eligibility limits.

Malloy said the workers referred for discipline are the ones that were “obvious,” but the state is still going over the applications and its possible more will turn up.

Department of Social Services Commissioner Roderick Bremby, whose department administered the $12.4 million program, said the names of those referred were discovered before the audit had begun. The names of the individuals and which departments they work in have still not been shared with the media.