The free movement of people between Ireland and Britain has survived centuries of tension and even terrorism, but that tradition is about to end with the severing of a special relationship between the two countries because of tighter security procedures.

Bertie Ahern, the Irish Prime Minister, confirmed in the Dáil yesterday that the Common Travel Area – which was created between the Republic of Ireland and the UK after independence – is to be dismantled with the construction of an electronic border control system by Britain by 2009.

Mr Ahern said that it was now only sensible for the Republic to follow Britain’s example and introduce similar security. The new border controls will collect and analyse passenger information, much of it in advance of travel in a similar fashion to controls already in use in the US.

Mr Ahern told Parliament that Britain began to tighten up border security after the 9/11 attacks in 2001.

“This is another move on that and they are putting in a huge amount of resources into their border control system.”

He said British officials were keeping the Irish Government fully informed of their plans. He added: “I see it as an opportunity for deeper cooperation, rather than the opposite.”

Nevertheless, it marks a fundamental change in the relationship between the two countries and raises awkward questions about the status of the Irish border between Northern Ireland and the Republic.

The UK’s only international land border is crisscrossed repeatedly by narrow country lanes. It occasionally cuts through the middle of villages and even buildings, potentially creating a security nightmare.

The problem was solved during the Troubles by the Army putting craters in many border roads and erecting guard points at major crossing points.

Mr Ahern said: “British authorities have no plans whatsoever to introduce any controls on the land border between North and South. I want to make that clear. All they are looking at is increased cross-border cooperation, targeting illegal immigrants.”

But the adoption of the new “e-Borders” regime has alarmed some Unionists. Jim Allister, a former Democratic Unionist and Member of the European Parliament said it would be “intolerable and preposterous if citizens of the UK had to present a passport to enter another part of the UK”.

The Home Office would only say yesterday that there “are no immediate plans to implement passport checks on passengers travelling from the Republic of Ireland to Britain”.

Given that the system is not set to begin until 2009, that potentially leaves a yawning gap in the Government’s new border security arrangements unless the question of the Irish border is addressed. Mr Ahern high-lighted that concern when he told the Irish Parliament that 90 per cent of all persons illegally entering the Republic were doing so across the border with Northern Ireland.

One Irish newspaper commented that “there have long been concerns that Islamic militants have been using Ireland as a backdoor entry system to the UK via the North”.

Before independence for 26 of Ireland’s 32 counties was agreed in 1922, British immigration law was enforced in Ireland in the same way as the rest of the nation.

In 1923 an informal agreement was reached between the fledgling Irish Free State’s Home Affairs Department and the Home Office to keep the status quo. What became known as the Common Travel Area allowed for free transit. But for the system to work effectively it has meant that the Irish government has had to shadow the UK’s immigration policies.

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