He told MSPs earlier this month that a final decision on proposals to move in-patient mental health services from Monklands Hospital to Wishaw General had been delegated to his deputy Michael Matheson to avoid a conflict of interest.
But it has emerged that Neil contacted NHS Lanarkshire through his officials just days after becoming Health Secretary in September, and expressed his reservations about the proposal.
Neil had already objected to the plan, as the local MSP, before becoming Health Secretary.
According to NHS Lanarkshire, Neil asked to review the proposals before they were submitted to its board members for a final decision.
NHS Lanarkshire has now agreed to review them in light of his feedback.
Labour said Neil's words in Parliament could not be squared with NHS Lanarkshire's account. They also accused him of trying to rewrite the proposals before they went to his deputy for a final decision, in a fait accompli.
Central Scotland Labour MSP Siobhan McMahon said: "It appears that Mr Neil has joined the growing number of SNP ministers who have misled Parliament.
''More importantly, it looks as if he has abused his position as Cabinet Secretary by meddling in NHS operational matters within his own constituency, and derailing a modernisation process which was a crucial part of renovating Monklands Hospital."
A Government spokesman said: "NHS Lanarkshire have yet to put forward their revised proposals to the Scottish Government. When a decision is required, the proposals will be put to Michael Matheson due to the issue concerning matters in Mr Neil's constituency."