The coup leaders placed tanks in strategic positions in Athens, effectively gaining complete control of the city. At the same time, a large number of small mobile units were dispatched to arrest leading politicians, authority figures, and ordinary citizens suspected of left-wing sympathies, according to lists prepared in advance. One of the first to be arrested was Lieutenant General Grigorios Spandidakis, Commander-in-Chief of the Hellenic Army. The colonels persuaded Spandidakis to join them, having him activate a previously-drafted action plan to move the coup forward. Under the command of paratrooper Lieutenant Colonel Kostas Aslanides, the LOK took over the Greek Defence Ministry while Pattakos gained control of communication centers, the parliament, the royal palace, and — according to detailed lists — arrested over 10,000 people.
By the early morning hours, the whole of Greece was in the hands of the colonels. All leading politicians, including acting Prime Minister Panagiotis Kanellopoulos, had been arrested and were held incommunicado by the conspirators. At 6:00 a.m. EET, Papadopoulos announced that eleven articles of theGreek constitution were suspended. One of the consequences of these suspensions was that anyone could be arrested without warrant at any time and brought before a military court to be tried. Yannis Ladas, then the director of ESA, recounted in a later interview that, "Within twenty minutes every politician, every man, every anarchist who was listed could be rounded up...It was a simple, diabolical plan".
Georgios Papandreou was arrested after a nighttime raid at his villa in Kastri. Andreas was arrested at around the same time, after seven soldiers armed with fixed bayonets and a machine gun forcibly entered his home. Andreas Papandreou escaped to the roof of his house, but surrendered after one of the soldiers held a gun to the head of his then-fourteen-year-old son George Papandreou. Gust Avrakotos, a high-ranking CIA officer in Greece who was close with the colonels, advised them to "shoot the motherfucker because he's going to come back to haunt you".
U.S. critics of the coup included then-Senator Lee Metcalf, who criticised the Johnson Administration for providing aid to a "military regime of collaborators and Nazi sympathisers." Phillips Talbot, the U.S. ambassador in Athens, disapproved of the coup, complaining that it represented "a rape of democracy", to which Jack Maury, the CIA station chief in Athens, answered, "How can you rape a whore?" Papadopoulos' junta attempted to re-engineer the Greek political landscape by coup.