Labour MSP Siobhan McMahon claims Mr Neil blocked plans to modernise mental health services by preventing proposals from being presented to NHS Lanarkshire.
A proposal to go before the health board last September included a plan for some patients to receive treatment in their homes and to transfer in-patient services from Monklands Hospital, Airdrie, to Hairmyres Hospital, East Kilbride, and Wishaw General. The plans had been approved the previous month by Nicola Sturgeon, then Health Secretary.
However, Ms McMahon says one of Mr Neil's first actions on taking up his new job in early September was to order a review of the proposals, preventing them going before the health board for approval.
The Central Scotland List MSP claims there was an conflict of interest because the proposals would lead to the closing of mental health services at Monklands, which is in Mr Neil's constituency.
Mr Neil is MSP for Airdrie and Shotts and the Ministerial Code says ministers must declare potential conflicts of interest surrounding decisions affecting their constituencies.
Miss McMahon said: "When I asked Mr Neil in the Scottish Parliament on December 19 when he last had discussions with NHS Lanarkshire about the modernisation of mental health services, he told me he had 'given responsibility to Michael Matheson' because he 'did not want any perception of a conflict of interest.'
"What he did not tell me was he had already interfered by preventing plans approved by Nicola Sturgeon from being ratified by the NHS Lanarkshire board.
"Now the whole modernisation process, which has already taken several years, has ground to a halt.
"The real losers are the thousands of people across Lanarkshire who will have to wait even longer to get the standard of mental health services they deserve."
Mr Neil's apparent intervention also angered Francis Fallon, chairman of mental health service Lanarkshire Links, who spent two years consulting with patients on the proposals. In a letter to Mr Neil this month, Mr Fallon said he was "greatly disappointed" at the intervention.
A Scottish Government spokesman said: "On September 26, Mr Neil asked officials to make his long-standing concerns about the proposed reconfiguration of mental health services across Lanarkshire known to the NHS board.
"His view was that acute mental health facilities would be best retained at Wishaw General and Monklands hospitals, and with a unit at Hairmyres.
"On September 26, after answering an oral question, Mr Neil was concerned that as Monklands was in his constituency, there could be a perception of a conflict of interest.
"To address this he agreed, that day that all matters related to Monklands should be dealt with by Public Health Minister Michael Matheson."