Cape Town — New political storms pelt at the South African government over its policy of apartheid. In a matter of just a few days last week:
* The second-largest church in the country, the Methodist Church, formally condemned apartheid (enforced social, economic, and political segregation of the races) as being ''sinful, the work of the devil.''
Methodist leaders have publicly recited a solemn oath to oppose the system and ''bring about a free and just southern Africa.''
* The Presbyterian Church, also a major religious body, now urges civil disobedience and has instructed its ministers to break certain apartheid laws, like those that make it illegal to marry people of different races.
* The government turned down the recommendation of its new President's Council to allow Coloreds (people of mixed racial background) to return to District Six, a section of Cape Town from which thousands of them were banished in the late 1960s.
The rejection has sparked criticism from some council members and from the Progressive Federal Party (PFP), the main white opposition party. The government only recently created the 60-member council - which has Asian and Colored members but no Africans (blacks) - and charged it to come up with a new constitution that would give Coloreds and Asian and Chinese South Africans some say in the running of national affairs.
A PFP spokesman says the government has made a ''mockery'' of its own vaunted ''instrument of reform.''
In fact, opposition politicians said the council was a waste of money from the start because it has no representatives of Africans, who form three-quarters of the population.
Meanwhile the government has called the Presbyterian Church's instructions to break the law ''malevolent instigation'' of unrest.
Some observers here view the rejection of the District Six recommendation as a catalyst to increase the civil disobedience movement.
The council had decided that government policy was wrong and that Coloreds should be allowed to return to District Six in the name of ''reconciliation.'' Many believed the government would agree. But the Cabinet turned down the major recommendation, agreeing only that a small part of the area should be zoned for occupation by Coloreds.