More than one hundred people are flagged to counter-terrorism units at Britain's borders every week.
The disclosure came as Sir Charles Montgomery, director general of the Border Force, was questioned about the exodus of Britons to fight alongside Islamic State in Syria and Iraq.
Police estimate that around 800 people have made the journey, with around half believed to have returned to the UK.
Sir Charles revealed his organisation is conducting hundreds of checks on routes into and out of the UK.
He told MPs: "On the inbound journey, my officers at the desks do a fair amount of their own personal questioning and profiling and on a weekly basis we have been on average referring over a hundred people from that process to CT (counter-terrorism)."
He stressed: "Let me make it clear - the vast majority of those are not of interest to counter terrorism police. A percentage get taken forward for further investigation."
Asked what the Border Force does in instances where individuals are suspected of returning from the region, he said that his organisation is not an "investigative or prosecuting unit" on such cases.
"We operate very closely alongside counter-terrorism police and we will refer those individuals for further questioning, which may be a very straight forward one minute discussion or it may go somewhat deeper," he added.
Giving evidence to the Commons home affairs committee, Sir Charles gave an insight into his organisation's role in the counter-terrorism effort.
Officers look at "advanced information of travel" to check for "known targets of interest", he said, adding: "The second thing we do even before any travel has been conducted is to look at travel patterns of people who are conducting certain behaviours or travelling in certain ways.
"The first is about targeting known individuals, the second is about targeting unknowns but people who are behaving in a way which is suspicious to the authorities."
Asked how many individuals in those categories are the focus of a "deeper delve" for information in a month, he said it was "in the hundreds".
He said there was another stage "at the moment of travel" when the Border Force or another agency "might choose to intervene" at check-in, adding: "We do conduct profiling and screening on targeted flights on routes that we've been prompted to look at even after check-in."
Sir Charles added that the scale and nature of work in relation to those coming into the UK was similar.
"We do the same degree of analysis before travel," he said. "We mount similar controls on the routes that we know are risky. Those are not necessarily the direct routes.
"We do that with our colleagues from counter-terrorism police or other agencies."
Sir Charles also told the committee that increased checking of freight and passengers were introduced on selected routes into the country within half an hour of news of the Paris attacks last month.
A similar approach was instigated shortly after on outbound routes, he said.
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