Portugal’s ‘neutrality’ appeared safe as houses on Monday when the Jerusalem Post revealed that Lisbon had refused permission to Israeli ‘cargo’ planes to use its airports at the height of the Lebanese conflict citing political reasons. But within 24 hours, evidence seemed to confirm that there had been direct flights operated by the US Central Intelligence Agency between Portugal and Guantanamo between 2002 and 2005.

Politicians returned to work this week and it initially appeared that thorny issues such as a referendum on abortion would be dominating their agenda.

But comments by former Minister of Foreign Affairs, Freitas do Amaral triggered piles of evidence pointing to Portugal’s complicity with Washington in the ferrying of terror suspects to Guantanamo, some of whom allegedly having been the victims of a series of human rights abuses.

Freitas do Amaral, who retired from Prime Minister José Sócrates cabinet earlier this summer citing health reasons, shook the foundations of his former cabinet when he ‘came clean’ in a letter to Portuguese Member of the European Parliament, Ana Gomes.

According to the former Jakarta attaché, the founder of the Christian Democrats in Portugal wrote “certain suspect planes passed through Portugal on a regular basis and for an extended period”.

In the clearest admission yet of collusion with the CIA, he is reported as saying that there had been “direct flights between Portugal and Guantanamo”, casting a dark cloud over Lisbon’s potential involvement with the United States’ ‘prisoners of war’.

Ana Gomes adds that alleged trips between Portugal and Guantanamo peaked between 2002 and 2004, and that it has been verified that these planes did “not stop in the country for short stopovers”.

The MEP has already called for a deep investigation into these allegations made by her former colleague, saying: “There is further evidence conforming the CIA used planes (that passed through Portugal) for the transport of prisoners”, adding however, and somewhat disbelievingly given its near impossibility, that “none of these prisoners have lodged a complaint against Portugal”.

However, Freitas do Amaral’s position has come as a surprise.

Last November, he issued a clear denial over allegations that CIA planes had landed in Portugal.

“We did not authorise the use of our airports, and if they were used, we did not know about it. I can guarantee that there are no records in the foreign ministry of any flights at the service of the CIA or other official United States agencies of prisoners to states where there could be illegal detention centres," Freitas do Amaral was reported as telling MPs on a parliamentary affairs committee late last year.

He later reiterated that there “was not a shred of evidence” found by investigators to suggest secret CIA planes had touched down in Portugal.

His position was also supported by the Defence Ministry, but when the situation threatened to go out of hand, the government said that while they could not give an undertaking for the actions of the previous pro ‘War in Iraq’ government, no such planes had landed in Portugal since March 12, 2005, the date when the Socialists took office.

Meanwhile, Portugal could face EU sanctions should it be found to have colluded with the CIA to the extent latest evidence is suggesting.

Any European Union member state found to have cooperated with the United States Central Intelligence Agency (CIA) in so-called “extraordinary rendition” flights would face sanctions, the European Parliament has repeatedly said in recent months.

Under the case law of the European Court of Human Rights, EU countries have the positive obligation to prevent human rights violations on their territory - and to carry out investigations “to ascertain whether their territory and their airspace” have been used in connection with human rights violations.

Last week, Visão magazine revealed that between August 2001 and November 2005, 131 planes operated by the CIA landed at Portuguese airports in Lisbon, Oporto, Ponta Delgada, and Santa Maria.

But in the clearest evidence yet that Portugal might have conspired with the CIA is an independent air traffic report released by EUROCONTROL, which regulates the air traffic of the 25 EU member states.

According to its records, it has verification of three direct flights between the Azores and Guantanamo, Cuba. The cargo and the passenger list remain unknown.

It is further suggested by the European Parliament, who publicised EUROCONTROL’s findings, that in addition to these three flights, an additional 18 landed in Portugal. They are suspected of being used for illegal activities by the American secret service.

None of these 21 flights (which besides Guantanamo, also touched down in Libya, Morocco and Tajikistan having stopped in Portugal) are logged with the National Civil Aviation Institute.

In the meantime, a parliamentary inquiry is taking place in Lisbon into this issue, though it is likely that few advances will be made between now and late October, when Portuguese government officials are set to appear before members of the European Parliament to explain Portugal’s alleged involvement with the CIA since 2001.