Britain needs to urgently clarify its position on security issues, senior European commission officials have warned, or risk missing out on vital new counter-terrorism tools.

The commission has been revamping systems to identify who is crossing borders into the EU, and help dismantle cells that are financing jihadist networks, tackle terrorists who use fake identities and upgrade Europol.

Yet the government’s ambiguity on how it intends to fit into Europe’s rapidly evolving security architecture has left officials wondering what, if any, cooperation will be possible in the future – prompting them to raise the possibility that the UK might end up on the outside of Europe’s counter terrorism apparatus.

An influential Conservative security policymaker, who created an EU counter-terror plan to collect personal data on passengers travelling to and from Europe, has also raised concerns that Britain will not be granted access to “critical” data unless it accepts a role for the European court of justice.

Lord Kirkhope of Harrogate, who was responsible for drawing up the Passenger Name Records (PNR) system during his time in the European parliament, said he feared that Theresa May’s ECJ red line could result in weakened security links.

His warning comes after terror attacks in London and Manchester that underlined the need to maintain security ties after Brexit which would allow the UK to track potential terrorists. The government will publish a series of formal position papers on Brexit this week, addressing the Irish border issue, a potential future customs arrangement with the EU and access to confidential documents.

But senior figures in the European commission remain baffled and perturbed that May has not yet offered a cogent position on how the UK intends to forge future security arrangements.

A senior commission source said: “Member states are increasingly serious about tackling terrorism, building a network of databases and agencies, and we are starting to see real results. But it’s not clear what the UK wants and, therefore, it’s not clear what cooperation will be possible in the future.”

Lord Kirkhope fears Britain will not be granted access to ‘critical’ data unless it accepts a role for the European court of justice. Photograph: Jonathan Goldberg/Rex Shutterstock

Britain’s most senior EU official has also stepped forward to warn that cooperation is essential in the fight against terrorism. Sir Julian King, the European commissioner responsible for security, said: “We are better able to tackle these [terrorist] threats together … we all stand to lose if we don’t find a way of maintaining as far as possible our deep cooperation.”

May remains determined to withdraw Britain from ECJ jurisdiction, which performs oversight of the European arrest warrant, along with other EU agreements including data protection laws.

The European arrest warrant is considered to be vital in apprehending and tracking terrorists, according to the European commission’s most recent assessment of European security measures. Data exchange is also an increasingly important part of member states’ approach to counter-terror activities.

Pointedly, the commission’s assessment also underlines the role of the European court, stating it is crucial to provide effective judicial control and that “compliance with fundamental rights is a key characteristic of EU security policy”.

The ECJ’s importance is also highlighted by a verdict on 26 July that the EU could not share PNR data with Canada, as that “would be incompatible with fundamental rights”.

Kirkhope, who was the European Conservative spokesman on security and justice in Brussels and who authored the PNR legislation, said the system allowed countries to exchange information in real time on “people of interest”.

He told the Observer: “I, and others who have been involved in the detailed work of putting in place in the EU a high level of cooperation in intelligence and police matters, believe that the only acceptable outcome of our present discussions with our European friends must be to replicate what we currently have in place and are currently perfecting.

“Throwing away the tools needed to build and maintain the structures we have planned and saying that somehow we can manage without them in future is nonsense.”

The European commission assessment, dated 26 July, also includes details of a cross-border exercise involving Belgian and Dutch police which replicated a series of synchronised terrorist attack on schools and which will inform practice among member states.