There is no evidence the US has used UK airspace for flights transferring terror suspects to countries where they could be tortured, the government says.
Mr Ingram said the UK should not "undermine" its allies
Armed Forces Minister Adam Ingram said it would be a diplomatic error for UK officials to board jets to investigate.
That would involve an "assumption" the US was not "being honest with us".
Speaking to the joint parliamentary committee on human rights, he said: "Why should we operate on that basis to undermine our allies?"
The government has acknowledged that six US planes linked by campaigners to "extraordinary rendition" flights have landed and taken off from UK airports on 73 occasions since 2001.
Under extraordinary rendition, intelligence agencies send terror suspects for interrogation by security officials in other countries.
Campaigners claim British airspace has been used for US flights transferring suspects to places where they could be tortured.
The UK government says there is no evidence of this.
Mr Ingram said in two cases before 1998, when the US had sought to transfer detainees via Britain, it had made open requests.
He said there was no reason to suspect it was now doing it secretly.