The roll-out of the flu vaccine nasal spray pilot scheme in Glasgow had been due to begin at city primary school on Wednesday, days after its launch by First Minister Alex Salmond.
But after parents at Glendale Primary in Pollokshields - which has a large number of Muslim pupils who cannot consume or use pig products for religious reasons - became aware of the ingredients, complaints were made and the scheme was put on hold.
In England, the Fluenz vaccine attracted criticism just a fortnight ago for the same reason, sparking accusations of insensitivity to Muslims, Jews and vegetarians, and concerns over the lack of information to parents.
NHS Greater Glasgow and Clyde (NHSGGC), whose area contains the overwhelming majority of Scotland's Muslims, said it had postponed the vaccinations "following concerns raised by a small number of parents".
The health board added that, in 2001, 100 Islamic scholars had agreed pork gelatine was permissible within a vaccine so there had been no need for advance publicity.
The city council moved to halt the programme within its schools after the complaints were made, with children at the pilot schools given letters last night informing them of the situation.
It will restart next week, with parents given the choice of an injection which does not contain the gelatine product. The roll-out is continuing elsewhere.
Glasgow councillor Soryia Siddique said: "Children's health and wellbeing is paramount. The serious failure is at a national level with regards to the clarity of the vaccine ingredient which should have been communicated to parents so they could make an informed decision."
Dr Syed Ahmed, consultant in public health medicine at NHSGGC, said: "We want to point out to parents and carers that the nasal spray vaccine contains a tiny amount of gelatine of pork origin used during the manufacturing process."
He said gelatine was commonly used in the manufacture of medicines and the trace in the finished nasal spray was a "completely changed substance".
He added: "In view of the 2001 agreement between the World Health Organisation and the Muslim scholars that pork gelatine was permissible within a vaccine there was no specific reference to this ingredient in the initial national communication that was produced for parents.
"However, in view of the concerns of a small number of parents we have updated our communication to confirm the inclusion of this ingredient in its manufactured state and advised parents they can request that their child can be provided with an alternative vaccination."
The vaccine is being offered for the first time to every child in Scotland aged two and three. Previously only children in "at risk" groups were offered the protection.
In all, about 120,000 children will be offered the vaccine, as well as 100,000 primary pupils in health board areas taking part in a pilot programme.
A city council spokeswoman said: "We asked for a delay ... to allow for additional information regarding the programme to be sent to families taking part in the immunisation pilot."
A Scottish Government spokeswoman said: "Many medicines, including vaccines ... contain traces of bovine and porcine gelatine. Gelatine is an essential ingredient to make the flu nasal spray vaccine effective. Many faith groups, including Jewish and Muslim communities, have approved the use of gelatin-containing vaccines."
Public health minister Michael Matheson added: "The Scottish Government very much appreciates the help and advice provided by Muslim councils in response to these concerns and a letter has been issued to all parents of Muslim children in Glasgow to offer reassurance about ... the Fluenz vaccine."