The apparently competing tactics come days after the Supreme Court ruled that O'Neill's ousted predecessor, Sir Michael Somare, is the rightful ruler of the South Pacific island nation, and a month before the beginning of national elections.
O'Neill had sought to reconvene Parliament to consider the Supreme Court ruling but most lawmakers are away campaigning.
A senior police source who declined to be named told the Australian Associated Press that the 30 officials who blockaded Parliament were not acting on the police commissioner's orders, and that he did not know whose orders they were acting on.
Police involved in the blockade said they will not allow Parliament to sit until after June elections.
A day earlier, Deputy Prime Minister Belden Namah led officers in the arrest of Chief Justice Sir Salamo Injia, one of three judges who on Monday affirmed an earlier ruling that Somare is the nation's legitimate prime minister.
O'Neill's government alleges the court is biased and is trying to interfere with the upcoming elections, which begin June 23 and last for two weeks.
Injia appeared in a court on Friday charged with sedition. He did not enter a plea. Hearing of the case was adjourned to July 25.
Parliament replaced Somare with O'Neill in August while Somare was getting medical treatment outside the country. The Supreme Court sided with Somare in December. In January, a supporter of Somare tried to take over the military with a small group of soldiers and ordered O'Neill to step down, but the effort failed and he was charged with mutiny.