Mr Neil pledged an improved pay deal and to review some of the pay arrangements which exist for health service executives at a conference of NHS managers.
Such pay rises have previously sparked controversy, with executives receiving £5000 and £10,000 increases.
But trade union Unison said they were entitled to pay rises like other health workers.
The NHS is under pressure from the ageing population and is struggling to hit key targets set by ministers.
Mr Neil made his comments in the text he sent to the conference after he was forced to pull out.
He said executive and senior management pay structures were put in place by the last administration and he understood "the concerns that now exist following several years of pay restraint".
Referring to a management pay circular due to be issued to Scottish health boards later this month, Mr Neil's speech said: "This settlement will be better than in recent years but I accept that questions will remain about whether the management pay arrangements introduced by the previous administration continue to be fit for purpose. I would like to be able to review elements of these within our vision for an integrated workforce."
John Restell, chief executive officer for Managers in Partnership, the trade union holding the event, noted NHS management pay and said: "The current pay system for senior managers in NHS Scotland is not up to the job and it could be challenged by people under equal pay legislation."
Nurses and other NHS staff employed on what is known as the Agenda for Change pay system received a 1% pay rise last April. Full details of the forthcoming management pay rise have not been revealed.
Dave Watson, Unison's Scottish organiser, said: "Health workers have suffered from real-term pay cuts for a number of years and managers are entitled to a pay rise like anyone else."