The head of Enterprise Cape Breton Corporation says he has done nothing wrong after complaints were raised that he hired along Conservative partisan lines.

John Lynn, CEO of Enterprise Cape Breton Corporation, is being investigated for "gross mismanagement" for allegedly using his position to hire three employees because they were connected to the federal Conservative Party.

Lynn is currently on leave with pay while the investigation proceeds.

"I was contacted by the ethics commissioner. I agreed to cooperate in a process and I am doing so. It was a recommendation that I take an administrative leave, it doesn’t come as any surprise to me," Lynn told CBC News.

Liberal MP Gerry Byrne of Newfoundland laid the original complaint. Mario Dion, the public sector integrity commissioner of Canada, said an investigation is warranted.

The appointment of Lynn, himself, is also under scrutiny.

Byrne alleges Ken Langley, Robert MacLean and Alan Murphy, along with Lynn, are all good friends of Defence Minister Peter MacKay. All were hired for jobs with ECBC. Byrne said the jobs were never posted.

But Lynn said he stands behind the appointments.

"Those individuals were hired as a result of real needs. Their qualifications were fine, they went through a process, they were hired. I feel entirely comfortable with those hires," he said.

Lynn is also being investigated for alleged mismanagement of funds at the Ben Eoin Marina, located about 25 kilometres outside of Sydney, N.S.

ECBC funded nearly the entire $4.8 million dollar cost of the marina without a strong business case, say critics.

Lynn — who wants to moor his own boat at the marina — defended the project, saying it’s money that has been well invested.

"I think in 25 years' time people will be looking back at that and saying, ‘What a great piece of strategic infrastructure and we’re very, very happy to have it.’ The marina project is a great project," he said.

Lynn said while the investigation is underway, he’ll enjoy some time off and plans to return to work once the investigation is completed.

The Atlantic Canada Opportunities Agency oversees ECBC, which is a Crown corporation.

A spokesman for MacKay on Tuesday pointed to a separate investigation into questionable hiring at ACOA, which found no political interference.

"It has previously been found that neither the minister nor his political staff influenced any public service decisions," Jay Paxton wrote in response to an emailed request for comment on the ECBC investigation.

In Question Period on Tuesday, Byrne asked National Revenue Minister Gail Shea — who is also the minister for ACOA —whether she is aware of the Dion investigation and whether she will cooperate fully in the investigation into the alleged inappropriate partisan hiring at ECBC.

"I can't speak to the details of any ongoing investigation," said Shea. "But I can assure the honourable member that although ECBC is an arms-length Crown corporation, that I expect officials to cooperate with any investigation that's ongoing."

Dion said his investigation would be done "as expeditiously" as possible, but did not offer a date by when it would be concluded.