Private emails obtained under Freedom of Information laws show the minister asked NHS Lanarkshire to tear up previously agreed plans and instead retain acute mental health beds at Monklands Hospital in his Airdrie and Shotts seat.
A few hours later he removed himself from the formal decision-making process in a bid to avoid claims he faced a conflict of interest, which would breach the government's strict ministerial code of conduct. He subsequently told MSPs he was not involved.
Neil Findlay, Labour's health spokesman, said: "Alex Neil must resign or Alex Salmond must sack him. He has been caught red-handed putting his political interests before the welfare of patients and misleading parliament.
"By issuing instructions that went against all professional advice, Alex Neil undermined the integrity of NHS staff and compromised patients' care.
"This disgraceful episode has proven that he is not fit to hold this office."
The role played by Mr Neil was revealed in e-mails obtained by Labour MSP for Motherwell and Wishaw John Pentland after an 18-month Freedom of Information battle.
They show how, on becoming Health Secretary in 2012, Mr Neil immediately halted plans that had been agreed by his predecessor Nicola Sturgeon. The move came as NHS Lanarkshire wanted to concentrate its acute mental services at Hairmyres and Wishaw hospitals and close 48 beds at Monklands.
Ms Sturgeon agreed the plan after she was told it was "not feasible" to retain beds at Monklands.
In July 2012 Ms Sturgeon's officials confirmed she was "content that NHS Lanarkshire proceeds" with the plan but asked that Mr Neil, as a local MSP who had publicly opposed the plan, be kept informed. A few weeks later, e-mails show, Mr Neil asked for the announcement to be delayed until he returned from holiday.
As a result, the health board agreed to delay a formal decision until its meeting in September. But on September 5, Mr Neil replaced Nicola Sturgeon as Health Secretary and immed-iately halted the reorganisation.
On September 26, 2012, his officials e-mailed the health board saying he was "clear in his view" that acute mental health facilities should be retained at Monklands.
The e-mail added: "The Cabinet Secretary has asked that you seek agreement from NHS Lanarkshire to reconfigure their plans accordingly."
Within hours he announced to MSPs: "NHS Lanarkshire is looking at the future of mental health provision throughout Lanarkshire and I believe it is revising its original proposal for the mental health service at Monklands with a view to retaining an acute mental health facility at the hospital."
Later that day he agreed with the then-head of the NHS, Derek Feeley, that "all ministerial matters relating to Monklands" should be dealt with by Public Health Minister Michael Matheson to avoid the perception of a conflict of interest.
In November, Mr Neil told MSPs he was not involved with the plans.
A revised plan, retaining some beds at Monklands, was announced in July last year.
Mr Neil's involvement was referred last year to Scotland's top civil servant Sir Peter Housden and Alex Salmond, the First Minister, who is ultimately responsible for ministers' conduct.
A Scottish Government spokesman said the First Minister had concluded that Mr Neil had acted properly, adding: "Mr Neil wished to review a number of key decisions, including these proposals. This is entirely legitimate for a new Cabinet Secretary."