The Russian Orthodox Church has demanded further testing of remains thought to belong to the son and daughter of Russia’s last emperor, Tsar Nicholas II, disrupting the government’s plans to rebury them in St Petersburg next month.

A working group created by the prime minister Dmitry Medvedev in July proposed on Friday to bury crown prince Alexei Romanov and his sister, grand duchess Maria, with the remains of their family in the iconic Peter and Paul Cathedral on 18 October.

But Medvedev’s spokeswoman later said the date for their burial would only be decided after additional consultation with the Russian Orthodox Church, reported news agency RIA Novosti. Church spokesman Vsevolod Chaplin said the working group had agreed to further testing of the remains to prove their authenticity.

“People have questions. We want further investigation so that any tests are done in the presence of church officials,” said Chaplin, adding that the church also wanted to do further testing on those remains already buried in the cathedral.

The church has refused to recognise the results of DNA testing that found the remains do indeed belong to the royal family, delaying the process of burying Alexei and Maria, which have been held in a state repository since 2007. The current head of the Russian Imperial House, grand duchess Maria Vladimirovna, also considers the burial of these remains “premature,” a spokesman told news agency RSN.

“These people have been canonised, and if their remains are found they will be considered holy relics that believers will pray to, for this reason it’s very important to make sure,” said Chaplin.

Several descendants of the tsar’s family who now live abroad had already been planning to come to Russia for the October burial before the latest complications arose.

“We’re very happy this story is coming to an end, but at the same time there’s bitterness over the fact that the church hasn’t recognised the remains,” Ivan Artsishevsky, a spokesman for the relatives, told news agency Interfax on Friday.

Tsar Nicholas II abdicated the throne in 1917, ending three centuries of rule by the Romanov dynasty, and sought asylum in Britain, but was refused by his cousin George V – Elizabeth II’s grandfather – over political concerns.

Held in captivity by the Bolsheviks, the family was executed by firing squad in the early hours of 17 July 1918 at a house in Yekaterinburg. Their bodies were thrown into a mineshaft, burned and then buried.

The first remains were found in Yekaterinburg in 1979, but remained buried until the end of the Soviet Union. In 2008, US and Russian experts confirmed that the remains unearthed in 1991 belonged to the tsar by matching DNA samples from the skeletons with those from living relatives and from objects such as a blood-stained shirt worn by Nicholas II.

The tsar, his wife Alexandra, daughters Anastasia, Olga and Tatiana and several servants were buried in St Petersburg in 1998 at a ceremony held by the president, Boris Yeltsin. Remains thought to belong to Alexei and Maria, who were 13 and 19 when they were killed, were discovered 43 miles away from the others in 2007. Russian investigators have ruled the remains are authentic based on genetic testing.

In a controversial decision, the Russian Orthodox Church canonised the Romanov family, which is revered by many right-wing groups but considered autocrats by others, in 2000.

The church has grown increasingly influential during the 15 years that president Vladimir Putin, who is often pictured with the patriarch, has been in office.