Rajavithi said they advised the Ruam Katanyu Foundation, which took Cholthicha Wannathip and her dead baby to the hospital, to go instead to Ramathibodi Hospital.
They said Rajavithi had no forensic doctors available to treat her, according to deputy permanent health secretary Vachira Pengchan, who quoted a report from Udom Chaovarindr, director of Rajavithi Hospital.
Dr Vachira claimed that neither the woman nor the rescue foundation staff had objected to the recommendation, while he expressed sympathy for Mrs Cholthicha and the loss of her baby.
However, the Rajavithi accounts differed from foundation staff members, who said the 31-year-old woman was turned down because there were no beds available.
Dr Udom told reporters that Rajavithi did not turn her down. The hospital always provided birth delivery services free of charge to poor people and migrants, he claimed.
"We did not reject the patient. We were on the receiving end of the process,'' he added.
The distraught new mother's plight became a talk of the town after it was posted on media networks on Sunday.
The native of Chum Phae district in Khon Kaen, who lives alone in Bangkok, was about six months pregnant went she went to a private hospital around 6am on Sunday, believing she might be about to give birth, and claimed benefits under membership of the Social Security Fund.
She was told by staff at the private hospital the SSF scheme did not cover her for the problem and it would cost her 15,000 to 18,000 baht.
Mrs Cholthicha told reporters from Ramathibodi Hospital on Sunday that she did not have the money and went home with medication to alleviate her pains. Hours later she delivered a baby boy by herself at home in Soi Inthamara 1 in Phaya Thai district.
Her neighbours called Bang Sue police for help around 3pm. Ruam Katanyu took her to Rajavithi about 3.30pm and then later to Ramathibodi Hospital, where she remains under treatment. Her condition is reported as safe.
She was found lying in bed at her house by rescue foundation staff, in an obviously weakened condition with the dead new born boy lying beside her, Pol Lt Col Darunee Thassana, of Bang Sue station said on Sunday.
The baby appeared to have died one or two hours before neighbours discovered her and called for help, the policewoman said.
The dead child had been sent to the Institute of Forensic Medicine at Police General Hospital for an examination to determine the cause of death, she said.
The SSF covers the cost of delivering a baby up to 13,000 baht, according to the SSF website. Mrs Cholthicha is registered with the private hospital she went to under the fund.
Suradej Waleeitttikul, deputy secretary-general of the Social Security Office, said Mrs Cholthicha had contributed to the fund for only four months and so was not be eligible for benefits for giving birth. According to the scheme's regulations, she must be a contributor for seven months before claiming the benefits.
"I think the main issue of this case is miscommunication,'' Mr Suradej said.
However, government policy since April last year gives citizens free access to emergency services at any hospital, including those under the SSF.
Tares Krassanairawiwong, deputy director-general of the Health Service Support Department, and Dr Vachira both said the department is investigating the private hospital's decision, whether the case was deemed an emergency and whether the hospital had properly advised the patient.
If her condition was considered an emergency, she would have been eligible for benefits, Dr Tares said. If the hospital did not act in accordance with the scheme's policy, it would be penalised, he said.
Jirasak Sukhonthachart, permanent secretary for labour affairs, said possible penalties for the private hospital include a warning and a limit on taking SSF subscribers. If a mistake is repeated, the fund could terminate its contract and the hospital's licence could be revoked.
The result of the investigation would be known in about a week, said Mr Jirasak. The Labour Ministry oversees the SSF scheme.
The dead baby would have been Mrs Cholthicha's fifth child.