The last remaining Little Penguin colony on the NSW mainland could be at risk if a tourism company's bid to change its operating conditions is approved, environmentalists and advocates say.

Mawland, which runs the Quarantine Station site at North Head in Manly, has applied for a raft of variations to its planning controls, including playing music in an outdoor area metres away from penguin nests, boosting visitor numbers and carrying out environmental audits less frequently.

The submission also includes a request to remove the NSW Parks and Wildlife Service as co-proponents of the site, which would mean that Mawland would accept primary responsibility for implementing the conditions of planning approval.

But environmentalists are concerned that such changes will threaten the endangered penguin colony, which is still struggling to recover from the loss of more than two dozen penguins killed by a fox last year.