Angrily brushing aside accusations that Syria kidnaped a Jordanian diplomat in Lebanon, Information Minister Achmad Iskandar today warned that Syria will press ahead with plans to "punish" top Jordanian leaders held responsible for instigating large-scale disorders here last year that led to a number of deaths and injuries.

Iskandar indirectly held the United States responsible for encouraging Jordan's alleged plans to destabilize Syria and pointed as evidence to the recent U.S. decision to provide new arms to Jordan "because of its supposed need in the struggle with Syria."

While proclaiming Syria's willingness to hold a dialogue with the Reagan administration about the stalled peace process in the Middle East, he said in an interview, "We are against American policy in the area," which he described as "Israeli policy implemented by the United States."

Noting statements by President Reagan, Secretary of State Alexander M. Haig Jr., and National Security Adviser Richard Allen, Iskandar said, "The new American administration is hostile to the Arabs and the Arab cause."

Other high government officials privately said that while Syria was still anxious to explore ways to renew the stalled peace process with the United States, the Reagan administration "did not seem to have gotten off to a good start."

Especially worrisome, they said, was Reagan's own description of controversial Israeli settlements in the occupied West Bank as "not illegal," a definition that "never had been used by any previous American administration."

Iskandar conceded that the outside world might find Syria's reasoning on the kidnaping affair and renewed tension with Jordon hard to follow.

But he insisted that "we do not feel we are in a dilemma or in an embarrassed situation" about either the kidnaping of Jordanian Charge d'Affaires Hisham Mohaisen or Syrias policy of reprisals against Jordonian leaders, especially against Prime Minister Mudar Badran.

Badran was held responsible for "supporting and supervsing" troublemakers who are officially described here as members of the right-wing fundamentalist Moslem Brotherhood.

"We will punish the killers," Iskandar said, "and the killers are known."

He indirectly confirmed reports that the Jordanians had captured a Syrian colonel in charge of a sabotage team near the Jordanian captial of Amman several days before the charge's abduction in Beirut Feb. 6.

While indignantly denying suggesting any "prisoner exchange" was envisaged, Iskandar warned that similar units would continue to be sent to Jordan.

Asked if he felt King Hussein of Jordan should also be held responsible for the disorders that last spring constituted the most serious internal challenge to President Hafez Assad's 10-year reign, the minister said "the king denies" any involvement. Asked if in the light of Syria's thesis that the king is aware of everything happening in his country whether he accepted the denial at face value, Iskandar replied, "You should ask King Hussein yourself."

Running throughout the three-hour interview was a tone of injured innocence about the kidnaping charges and cold determination to "kill all those responsible for spilling innocent Syrian blood," whether they were in Iraq, Jordan "or anywhere else."

Noting that Syria had denounced the charge's kidnaping "eight times in eight days," Iskandar said Syria did not want relations to deteriorate further with Jordan.

But is was up to Jordan to take in initiative in seeking to improve the badly strained ties, he argued, just as he insisted it was Jordan that had initiated their deterioration.

Despite his sometimes truculent tone, Iskandar at no point suggested that Syria plans to send troops to the Jordanian border as it did last November.

Saudi Arabia mediated the dispute then, and the troops were withdrawn.

Other high government officials acknowledged privately that the troop movement at that time "did not serve President Assad's image and that it would have been better not to have done that."

They also stressed that Assad was "100 percent against" the Beirut kidnaping, was "very upset" by the accusations of Syrian responsibility and had personally reassured prominent visitors that "Syria had nothing to do with the Mohaisen affair."

"We know now that all the appearances are against us," these officials said in deploring that Syria would be seen as the Middle East's main troublemaker.

But they underlined that Assad had been "terribly hurt by the Jordanian government involvement" in the widespread disorders last spring "which had left very deep scars."