The start of the series, which sets eight British citizens the task of entering the UK using illegal means, was dropped from schedules last week.
But it aired on Monday evening and the Home Office said it was “insensitive and irresponsible” to show it so soon.
Channel 4 argued the show was “a matter of urgent public interest”.
The programme aimed to test the UK’s border security by following the progress of eight people trying to smuggle themselves into Britain from various points in Europe without showing valid documentation.
As the eight are all British citizens, who would be able to produce valid passports if challenged, they are not committing a criminal offence, the Home Office has confirmed.
Among those featured in the first episode was a pensioner from Reading who hid inside a mobile home and successfully passed through French and English border controls.
The show’s producers say they found major weaknesses with border checks and UK audiences should be shown these flaws.