Manila — Philippine President Ferdinand Marcos seems to be alienated from his people as has never happened before in his 18-year rule. This has placed Mr. Marcos on the defensive in two recent national television and radio appearances in which he has affirmed that he will not leave the presidency, despite widespread calls for his resignation. He has also blamed opposition leaders for blocking the work of the commission he created to investigate the assassination of Benigno Aquino.
Last week's large anti-government rallies in Manila, several of which erupted into violent confrontations with police, has underscored popular discontent with Marcos's rule, a discontent which has spread to Manila's middle class but not, as yet, to the countryside. An overwhelming number of Filipinos point accusing fingers at the Philippine government for Aquino's murder.
Meantime, dozens of US congressmen have called on President Reagan to cancel his Manila visit, now expected Nov. 5 and 6.
In the midst of the government's legitimacy crisis, Marcos has had difficulty expediting the investigation of the killing. He hopes the probe will vindicate his government and its account of how Aquino was shot minutes after he was taken into military custody at Manila airport on Aug. 21.
In a nationwide broadcast Monday, Marcos indicated the urgency of the resumption of the commission's work, which has been suspended for more than two weeks, and now is due to recommence on Oct. 10. He said that the commission will continue its task despite the absence of its chairman, Enrique Fernando, who is also chief justice of the Supreme Court. Mr. Fernando has withdrawn from the commission pending resolution of three cases filed by the political opposition before the Supreme Court questioning his chairmanship of the fact-finding body.
(An opposition coalition spokesman said Tuesday that witnesses who dispute the government's account of the assassination are afraid to come forward at the commission's hearings despite assurances of their safety, according to UPI.
(''Under the climate of fear that is pervading this country, these witnesses cannot testify because they are afraid of reprisals,'' said Antonio Alano, of the 12-party United Nationalist Democratic Organization.)
Last Sunday, a haggard-looking Marcos also went on a nationwide broadcast to warn protesting businessmen, churchmen, and youth that they would be prosecuted for their involvement in last week's rallies. Marcos warned the ''arrogant rich and oligarchs'' who use criminal elements in demonstrations in Makati, Manila's banking and business district, to create a revolutionary atmosphere.
The protests of the Filipino middle and upper classes is considered the most significant political development in the country in years. They had been most tolerant of the government, and for them to protest against Marcos's continued rule means the loss of an important ally for the President.
Another significant point about the rallies of the last two weeks is the age of the protesting youths. Most were only 7 or 8 years old when Marcos declared martial law in 1972 and never really knew Aquino as an active politician. In the last 11 years, they have been educated in the ideology of Marcos's ''new society ,'' both through the school curriculum and through the government-controlled media.
A spokesman for the powerful Roman Catholic church in the Philippines told The Christian Science Monitor that something has snapped, causing students to break their long silence. ''What caused the snap is the blatantly repressive atmosphere created by the government,'' he said.
It is now the middle class, businessmen, and the new crop of students which opposition leaders think could form the bulk of an effective protest group against Marcos.