The deadline ended a day after riot police received orders to remove the anti-government crowd from the compound of the prime minister's office and clear nearby public roads.
But moving the crowd, which had set up makeshift barricades of car tyres, razor wire and steel crash barriers on access roads leading to Samak's office, will prove to be a major task.
The alliance is seeking to force the present government to step down, accusing it of corruption and of serving as a proxy for Thaksin Shinawatra, the former PM who was ousted in a 2006 coup and now facing several corruption charges.
Samak however has refused to resign but said the authorities would avoid using force against the demonstrators, alleging they were trying to provoke the military.
"They want bloodshed in the country," he said. "They want the military to come out and do the coup again."
On Wednesday tens of thousands of PAD members also defied a court order to immediately abandon their two-day siege, or face legal and police action.
Major General Suraphol Tuanthong, the deputy police spokesman, said warrants were issued for nine protest leaders on charges of insurrection, conspiracy, illegal assembly and refusing orders to disperse.
Insurrection, the legal equivalent of treason under Thai laws, carries a maximum penalty of death or life imprisonment.
PAD, which is aligned with conservative factions of the monarchy and the military, has led anti-government protests across Bangkok in recent months to demand Samak's resignation.
The group also proclaims itself a defender of revered King Bhumibol Adulyadej against a supposed Thaksin plan to turn Thailand into a republic - a charge vehemently denied by both Thaksin, now in exile in London, and the government.