A survey of staff at Natural Resources Wales (NRW) suggested only 10% felt it was well managed.
Mr Jones told AMs that chairwoman Diane McCrea and chief executive Emyr Roberts "must drive positive change from the top".
Plaid AM Bethan Jenkins said the survey indicated "a problem with senior management".
Natural Resources Wales (NRW) is run at an arms length from Welsh Government, but is funded by it.
During First Minister's Questions in the Senedd on Tuesday, Mr Jones said Environment and Rural Affairs Secretary Lesley Griffiths had met the chair and chief executive of NRW and "outlined her disappointment with the figures".
She "stressed the importance of proper staff engagement," he said.
Responding to a question from Ms Jenkins, the first minister said: "There is a responsibility on the chair and chief executive to make sure staff feel valued.
"I noticed from the survey that overall staff were more satisfied than they were last year," he added.
"But it is right to say that when we drill down underneath those figures, in terms of perceptions of management for example, career development, and understanding of the organisation's direction, that the figures were not as good."
Ms Jenkins, Plaid Cymru AM for South Wales West, said: "The survey results clearly indicate there is a problem with senior management and it's far worse than last year."
Just 11% of workers who answered NRW's 2016 People Survey said they had confidence in senior managers' decisions.
Some 47% said they felt valued for the work they do, down 7% on 2015.
In the wake of the findings NRW chief executive Emyr Roberts said senior managers needed to do more to support staff.
Bosses at Wales' environmental watchdog need to ensure staff feel valued, First Minister Carwyn Jones has said.