New Delhi — Several days after the Indian Army invaded the Sikh religion's holiest shrine to root out militants, Amritsar is a ghostly city. Its only sounds are the strains of gurbani prayers and the shrill exchanges of gunfire between the Army and Sikh extremists loyal to their leader, Sant Jarnail Singh Bhindranwale, who was killed in the June 6 assault on the Golden Temple.
The repercussions of the Army raid continue to be felt:
* Up to 400 Sikh soldiers were said to have staged a mutiny over the weekend at the large Army cantonment of Gangan-agar, in the desert of Rajasthan State. The Ministry of Defense denies there was a mutiny, but does concede that some 100 Sikh extremists, dressed as Indian Army enlisted jawans, infiltrated Army units guarding the Pakistani frontier and called on them to revolt. At least three Sikhs were killed in clashes at front-line positions.
* India's first Sikh President, Zail Singh, is reportedly contemplating resignation after a visit Friday to the Golden Temple, the scene of the Army raid, which, coupled with other Army thrusts into the Punjab State, may have taken as many as 1,000 lives.
* The Army commander of ''operation Punjab'' says he is convinced that the Sikh militants had received large caches of weapons via Pakistan. He also claims that a sizable number of Pakistani passports were found in Sant Bhindranwale's basement command, and that two Pakistani nationals were killed during the Golden Temple assault.
* The Army says that nearly 500 bodies had been cremated at the Golden Temple alone, including those of Sant Bhindranwale and a number of his aides. The Sikh religious hierarchy has lodged an official protest, insisting that the bodies should have been turned over to them. This adds yet another dimension to Sikh charges of Hindu sacrilege.
It has been a week now since anything has moved in or out of Punjab.
The most prosperous state in India is battle-scarred and shocked. In New Delhi, there has been remarkably little reaction from India's opposition political parties. Editorials in the English-language press have been largely restrained.
''It was a dreadful, unenviable decision which (Prime Minister Indira) Gandhi had to make,'' one diplomatic official said. ''And, perhaps, in the final analysis, she did too much, too late.''
The Sikh authority and historian, Kushwant Singh, said: ''What happened inside the Golden Temple is a turning point in modern India's history.
''The idea of Khalistan - a separate Sikh nation - always odious to me, has suddenly and unexpectedly, sprung very much alive.'' The concept of Khalistan - ''the land of the pure'' - had, until last week's mayhem, its greatest and most vocal support in London and the US.
In his two-year campaign for greater Sikh autonomy, Sant Bhindranwale had flirted with the idea of breaking away to form a separate nation but had never openly endorsed it. Such a nation would include all of the Punjab - the country's breadbasket, on which India is dependent for food - and parts of the present states of Haryana, Rajasthan, Uttar Pradesh, and Himachal Pradesh.
At the fashionable New Delhi golf club, a watering ground for only the strictly upper class, turbaned men and bejeweled Sikh women wore black mourning bands. They are the elite of New Delhi who, only last week, shuddered at the mere mention of Sant Bhindranwale's name. Today, they are aghast at the violation of Sikhdom's most holy shrine.
Speaking sadly from his book-lined study, Kushwant Singh said that by ordering the preemptive military strike, Mrs. Gandhi had eliminated the representative of the Sikh community with whom the government could talk.
''No Sikh of any credibility would dare to go and negotiate with her now,'' agreed the respected editor of the Tribune group of publications, Satindra Singh.
Meanwhile, inside shuttered houses, Punjabis waited in a thousand villages and towns as the second phase of ''operation Punjab'' got under way, with the Army sweeping into the heartland of India's lushest state. They are intent on ferreting out any remaining extremists and hidden stores of arms. At least 1,500 Sikh militants have already surrendered or been rounded up - 465 of them inside the Golden temple complex itself.
But, with acts of violence and several exchanges of gunfire continuing Sunday , it is suspected that as many as 300 of Bhindranwale's loyalists were able to escape from the Golden Temple.
One of the more challenging questions now confronting Indian intelligence officials is where the extremists got their weapons, and how they had established links with the international arms markets in Europe and the Middle East.
The general heading the Punjabi operations has already said that large numbers were smuggled in through Pakistan. But, in the sweep of the Golden Temple, vast caches of machine guns, rocket launchers, antitank missiles, mortars, Sten guns, and grenades were discovered, some in buildings, some in labyrinthine by-ways. Some had Pakistani markings. Others bore the trademark of American manufacture. Still others were from China, Sweden, and Canada. And, according to one security official, others were clearly from Indian Army stocks.
Zail Singh, who has been India's President since July 1982, returned to the presidential palace from Amritsar reportedly shaken and outraged. He immediately ordered official mourning for his largely Sikh staff, and canceled all public appearances. He did not meet immediately with Mrs. Gandhi, who was on a trip to Rajasthan.
The President was particularly angered, according to a friend, by the damage done to the second most sacred shrine in the Golden Temple complex, the Akal Takht. It houses the holy book - the ''Granth Sahib'' - and is the seat of Sikhdom's five head priests.
This limestone building just behind the Golden Temple itself was Sant Bhin-dranwale's headquarters. The building suffered artillery hits as Bhindranwale and his key aides held off the Army for 24 hours from their basement command.
Harchand Singh Longowal, leader of the main Sikh political party, the Akali Dal, also kept his headquarters at the Golden Temple, but left the complex before the Army assault.