Afghan Regime Hit by Desertions. Civilians and militiamen accept guerrillas' amnesty offer and flee from government side. CROSSING OVER TO THE MUJAHIDEEN

AFGHAN government troops are bracing for a resistance assault expected within weeks on Jalalabad, Afghanistan's third largest city. And already, refugees - some of them former government militiamen and their families - are fleeing Jalalabad and nearby communist-held towns at the rate of several hundred a day. These departures are an indication that major government strongholds are beginning to crumble under sustained military pressure and sieges by the mujahideen (as the guerrillas are known).

The resistance has been tightening the screws on Afghanistan's communist government since Feb. 15, when the last of the Soviet Union's 120,000 troops pulled out. In the two weeks since, thousands of government soldiers and militiamen are reported to have defected to the guerrilla side.

According to resistance sources, entire units and companies have deserted from Kabul, Jalalabad, Kandahar, and other areas. One unconfirmed report says mass defection from the northern provinces total over 10,000 men.

At Angur Bandakhana, a once-bustling bazaar center less than four miles from Jalalabad and completely abandoned save for one family, Afghan guerrillas stopped to check the papers of two departing regime supporters last week. The men - one elderly with a thick beard, the other cleanshaven and in his late teens - were nervous but talkative as they clutched their letters of safe conduct provided by other guerrillas.

Guerrilla commander Akhtar Mohammed, a high-school principal in Jalalabad before war broke out a decade ago, refused to shake hands with them. Instead, he fired off questions about conditions up the road, where the forward positions of the government security forces are located. He also queried the two men about the situation in Jalalabad and their reasons for deserting.

Haji Gul, the elder militiaman, who was making his way to Pakistan with his two wives and a bevy of small children, mentioned an amnesty offered by the guerrillas.

The younger man, Rahman Gul, drew a laugh from the guerrillas when he explained that he only joined the militia to obtain a Kalashnikov assault rifle.

``I wanted to sell it to buy a wife in Pakistan,'' he said. In towns and villages previously controlled by the government, numerous men such as Gul had joined the Kabul regime more out of tribal links or financial incentives that out of ideological conviction. Compared to Army conscripts and mujahideen, militiamen are extremely well paid.

The guerrillas' offer of amnesty to regime supporters is part of a strategy to minimize fighting and destruction - and thus also prevent loss of support among war-weary civilians. Recently, reports of guerrilla atrocities in captured areas have made many urban dwellers, even those sympathetic to the resistance, nervous about the mujahideen.

Aware of such abuses, concerned resistance commanders have appealed to the local city populations, as well as government officials and members of the armed forces, to quit the Soviet-backed regime of the People's Democratic Party of Afghanistan (PDPA) headed by President Najibullah. Top guerrilla leaders such as Abdul Haq, whose men operate in and around Kabul; Ahmed Shah Massoud from the north; and Ismail Khan from Herat and the west, are hoping to provoke internal revolts and a coup rather than having to launch frontal assaults in their campaigns against the cities.

According to both Western diplomats and resistance sources, the PDPA regime has been seeking to strengthen security in urban areas. Party officials, civil servants, and civilians have been given arms. The men are deployed mainly in the security belts established around the towns, and female PDPA volunteers have been posted outside government buildings and along street intersections, the sources say.

MORALE, however, is said to be extremely low.

``There is no motivation. The soldiers have nothing more to fight for now that the Soviets are gone. Many are just waiting for the chance to join us,'' Commander Mohammed said, as we toured a series of ghost towns and villages now under guerrilla control on the outskirts of Jalalabad. According to the guerrillas, a recent party meeting in Jalalabad broke up in disarray, with hard-liners executing half a dozen Afghans who had called for negotiations with the resistance.

As many as 15,000 to 20,000 people are believed to have fled Jalalabad (pop. 60,000) since the beginning of this year. In recent days, the regime has begun trying to prevent civilians and militiamen from abandoning ship. Reportedly, only those bearing official permits are allowed through heavily guarded checkpoints.

Land mines, too, prevent people from escaping. Sowed by the millions throughout the countryside by Soviet and Afghan troops, the mines make travel off the major roads dangerous. Yet judging by the trickle of refugees who braved the mines and were encountered by this correspondent last week near Jalalabad, the measures appear to be having only limited effect.

From hidden viewpoints along the nearby Kunar River, one could observe government tanks, armored personnel carriers, and other vehicles move along the roads in clouds of dust. Periodically, government troops or militia units would launch mortars and rockets which exploded among the abandoned farms.

With most of the civilians gone, groups of mujahideen have set up bases in the abandoned adobe compounds around Jalalabad. Only the occasional family or ``greybeard'' has remained to care for fruit orchards and fields planted with winter wheat. Now six inches high, crops will wither away for lack of irrigation unless the people return.

``Inshallah [God willing] these government people will see how senseless it is to go on fighting,'' says one commander.

``But,'' the guerrilla continues, ``some of them don't care. So this land may not see peace for much time to come.''