Correspondents say he is unwilling to grant US soldiers immunity from prosecution and is unhappy that Afghans are still being held in US-run military prisons on Afghan soil.
Meanwhile, Germany's Foreign Minister Frank-Walter Steinmeier is expected to raise the issue of "secret" prisons in talks with US Secretary of State Condoleezza Rice in Washington on Tuesday.
The UK Foreign Office has confirmed that Britain will be writing to the US, on behalf the EU, to clarify the reports of secret prisons, which were reportedly set up after the 11 September 2001 attacks.
"The minister told us that the Ministry of Justice is negotiating with the Treasury for monies to replace prisons in order to bring the cost of the prison estate down, " he added.