Complex sentence: At this stage the government proposed to pay for the building outright in order to maintain secrecy over the intended use of the site--at this time the existence of MI6 was not officially acknowledged.
Split into simpler sentences: At this stage the government proposed to pay for the building outright in order to maintain secrecy over the intended use of the site. It is important to note that at this time the existence of MI6 was not officially acknowledged.