The individual has been arrested and deported.
The UK Border Agency - which is tasked with tracking down illegal immigrants - has admitted that one has been working in its offices.
An agency spokesman said the person was employed by a contractor and managed a team of cleaners at its Liverpool base.
But despite a crackdown across government in the wake of a series of blunders last year, the breach was only discovered a few weeks ago.
The Tories said the revelation showed the government's "serial incompetence".
The news is embarrassing for the UK Border Agency which has recently been threatening to "name and shame" companies which give jobs to illegal immigrants.
The individual was arrested on 25 June for "illegal entry without leave", and has been deported, the spokesman said.
It is not known how long they had been working at the public inquiry office, which considers "straightforward" immigration applications.
It comes more than two years after five illegal immigrants were found working at immigration offices - one of the incidents which led ex-Home Secretary John Reid to describe his department as "not fit for purpose".
Since then, ministers have admitted that thousands of illegal immigrants were granted licences to work as security guards, ending up at Scotland Yard, Whitehall departments and even protecting the prime minister's car.
Shadow home secretary Dominic Grieve said: "This is becoming a regular occurrence showing serial incompetence on behalf of the government.
"How can the agency in charge of border security lecture business about employing illegal immigrants when it cannot even get its own house in order?"
A UK Border Agency spokeswoman said: "A cleaning manger working for a contractor was arrested for illegal entry without leave and has now been removed from the country. We remove one person every eight minutes."