Embroiled in the controversy is The Railway hospital in Volgograd, in Russia's south, that the UK drug giant contracted for a reported $50,000 (€38,000) to run clinical trials on its behalf, in the absence of any suitable contract research organisations (CROs) in the region.
Testing at the site has now been suspended as the local Russian authorities have stepped in to investigate the claims.
Meanwhile, the hospital and GSK are both appealing against the decision.
It is alleged that clinical trials, which were approved by the Russian regulatory authorities in 2005, were carried out by the hospital on healthy children as well as those with pre-existing health problems, when a condition of the trial approval was that only healthy children could take part.
It is also alleged that a handful of children have experienced health complications and/or developed learning difficulties after receiving the vaccines.
In addition, Russian prosecutors claim that many parents were not properly informed that their children were taking part in a clinical trial and thought the vaccinations were routine.
The tests in question were part of a global Phase IV clinical trial programme for three of GSK's paediatric vaccines - Varilrix for chickenpox, Priorix for measles, mumps and rubella (MMR) and Priorix Tetra, a combination of the two.
5,700 toddlers across Europe were involved in the programme, 1,000 of which came from Russia and roughly 100 from the Volgograd site.
Responding to the allegations, GSK strongly denied any wrongdoing or breach of GCP.
"As far as we are concerned these reports are untrue and unfounded," a GSK spokesperson told Outsourcing-Pharma.com.
"The allegations arose through anonymous emails sent to the Russian media."
However, the spokesperson said they "would not like to speculate" as to why somebody would do this.
According to the spokesperson, GSK has now conducted its own internal audit of the site which showed that informed consent had been given by all parents and doctors involved in the trial and no adverse effects had been reported through the "normal channels."
"If any child had suffered an adverse event there is no reason why a parent wouldn't report it," said the spokesperson.
"We're extremely concerned about these unsubstantiated and untrue allegations."
GSK said it is now waiting to hear back from the Russian prosecutors regarding the findings of their investigation.