"We truly apologise. That should not have happened and we don't approve of it," Weng Tojirakarn, a protest leader, said.
Weng acknowledged some red shirts have a "cowboy attitude" that presents an image problem for the movement, which is already struggling to get support from middle-class Bangkok.
The protesters later cleared part of the road in front of the hospital to allow access for ambulances and patients, and erected a new barricade of tyres and bamboo poles on the other side of the road.
This was the second setback in a week for thousands of mostly rural and urban poor supporters of Thaksin Shinawatra, the former prime minister, after security forces stopped an attempt to hold "mobile rallies" on Wednesday.
The protesters have set up a three square-km fortified encampment in Bangkok's shopping district, which has forced the closure of several upscale department stores and hotels, has become a tented city within a city.
"It's not necessary for me to condemn [the hospital break-in] since Thai society and the world community have already done that," Abhisit Vejjajiva, the prime minister said.
He said that the the government would "not allow any movements that pose threats to the public".
Despite such warnings, the Red Shirts have defied authorities at every turn, entering the Parliament building, laying siege to a telecommunications complex, blocking roads and staging mass motorised rallies since March 12.
At least 27 people have died and nearly 1,000 have been injured in violence since then.
Earlier on Thursday pro-government protesters called on Abhisit to take concrete measures against the opposition demonstrators.
About 1,000 so-called yellow shirts gathered outside the 11th Infantry Regiment headquarters demanding that he army act against their rival red shirts.
"They are going there to deliver a letter to the prime minister and also the head of the army to say that they want concrete measures, harsh measures in place to deal with the red shirts, to get rid of them from the streets," Al Jazeera's Wayne Hay, reporting from Bangkok, said.