Iranian troops moved into this provincial capital today in an effort to put down a bloody outburst of minority nationalism that intensified threats to Ayatollah Ruhollah Khomeini's control of the country's border regions.

Before troops loyal to Khomeini arrived, masked snipers firing automatic weapons from city rooftops killed a member of Khomeini's Revolutionary Guard and wounded at least three others, bringing the casualty total for the three days of fighting to 12 dead and 73 injured.

The atmosphere remained tense tonight as sporadic shooting and street-fighting persisted in the latest regional outburst aimed at least partly at the Khomeini regime. Soldiers in tanks and armored personnel carriers patrolled the city, trying to enforce a cease-fire signed by warring parties yesterday.

With the third day of unrest in this southeastern province of Baluchistan-Sistan on the Pakistani border, and smoldering tensions in two populous northwest provinces, Khomeini has serious problems distracting him from the situation of the 50 Americans being held in the U.S. Embassy in Tehran.

Government forces were sent to the capital of the mountainous, desert-skirted province today after Khomeini's regional trouble-shooter, Ibrahim Yazdi, failed to negotiate an end to fighting between the Sistani and Baluchi tribes, who belong to different Islamic sects.

Traditional ethnic rivalry intensified earlier this month when a new constitution approved by a national referendum made Shiite Islam the official religion of Iran. The Baluchis, Sunni Moslems who greatly outnumber the Sistani Shiites here, largely boycotted the election.

Another irritant was the arrival of Khomeini's force of Shiite Revolutionary Guards, a militia that roams the streets with automatic weapons and presents a constant reminder to the Baluchis of their minority religious status and their dislike for the central government.

Just what sparked the recent violent outbursts is a matter of dispute. The provincial governor, Habib Jaririe, said the chronic tension between the economically, socially and religiously disparate groups has been fanned by leftist groups who hope to topple Khomeini.

Yazdi, a kind of ombudsman charged with resolving differences in the provinces, had a different explanation. Emerging from several hours of negotiation with Sistani and Baluchi leaders at a high school today, he told reporters that "foreign elements" were responsible for stirring up longstanding conflicts between the two tribes.

Yazdi said the alleged instigators were arrested today but he refused to identify them or give their number or nationality.

When asked if such secret arrests were reminiscent of SAVAK, the hated secret police of the deposed shah, he replied, "We are governing our own affairs."

Throughout the last several weeks of ethnic unrest in Kurdistan and Azerbaijan -- the provinces in the northwest that are seeking autonomy from the central government -- Khomeini and his representatives blamed the problems on "foreign agents," especially the CIA.

The Baluchis, a largely nomadic people surviving on date farming and smuggling, and the Sistanis, a better educated and wealthier class of farmers and businessmen, began fighting Thursday when several hundred residents of Zahedan began walking to a mountain retreat to hear a conciliatory speech from Yazdi.

Proceeding up the mountain path, the Sistanis began chanting slogans supporting Khomeini's selected governor, Jaririe and the ever-present Revolutionary Guard, according to Jaririe. The Baluchis then began yelling insults against the governor and the militiamen.

Suddenly, the shouting turned into pushing, stone-throwing and shooting, leaving three dead and 44 wounded. Eight more died and 23 were wounded yesterday as fighting continued in the narrow streets of this poor capital city of 60,000.

After his meeting today, Yazdi said both sides agreed to a cease-fire and approved of military intervention to enforce it. The agreement, he said, was signed by the province's two turbaned religious leaders -- Moulavi Abdol Aziz Mollazadah of the Sunnis and Ayatollah Mohammed Kafami of the Shiites.

Even as he spoke, however, gunshots could be heard a few blocks away and shouting by street mobs continued for several hours amid military loudspeakers blaring, "We are the Army and we are in control of the situation. Go to your homes."

Tensions were running high all day as shopkeepers and residents fled the commercial center of town shortly after noon. Cab drivers refused to go into most sections of the city, and one quickly threw his vehicle into reverse when asked to enter a certain quarter.

Jittery Revolutionary Guards, ensconced in a heavily protected building surrounded by sandbags, contributed to the uneasiness by a prominent display of arms. Fingers were kept near the triggers of their submachine guns ready for the slightest provocation.

When a car backfired near the guard headquarters, one especially nervous young militiaman dropped his pistol, then his hat and finally his pistol again before recovering and running full speed in the direction of the misfiring vehicle.

Communications from the city were frustrated for most of the day because of telephone line breaks.