Chief executive Jonathan Parry, chief operating officer Sheilah Finnegan and human resources boss Sharon Partington have been temporarily excluded.
The trust said it was investigating a "serious employment issue".
No aspect of the complaints or the investigation relate to patient care or safety, said a spokeswoman.
Deputy director of performance Richard McCarthy has also been temporarily suspended.
The decision to suspend the four employees follows an independent external investigation by the Good Governance Institute but was "not a disciplinary sanction", added the trust spokeswoman.
Sue Musson, chair of the trust, said: "An internal investigation will now begin in line with our disciplinary policy."
Southport councillor Tony Dawson said the suspension was "thankfully rare" and he hoped for an "early conclusion to the matter".
"This has come at a difficult time for the Trust. The Clinical Commissioning Groups locally have just required them to bid to retain the Community Nursing contract and there is a major financial deficit to address.
"As a former NHS whistleblower myself, I recognise the importance of people being able to raise their concerns without improper backlash.
Indeed, I referred a whistleblowing message to the hospital managers only last week."
Three executives have been drafted in to help run the trust, including Ann Marr, chief executive of St Helens and Knowsley Teaching Hospital NHS Trust.
Last November, an inspection by the health watchdog Care Quality Commission (CQC) found the trust required improvement.
Southport and Formby District General Hospital and Ormskirk General Hospital were ordered to improve after staff skill levels in A&E at both sites fell below "a consistently safe service".
Maternity services at Ormskirk were rated "inadequate" while the North West Regional Spinal Injuries Centre, in Southport, was also found to have staffing levels "significantly lower" than national guidelines recommend.
Three senior leaders of Southport and Ormskirk Hospital NHS Trust have been suspended after complaints by whistleblowers.