When fiscal 1982 dawned Oct. 1, only one branch of the federal government was funded on a permanent basis for the new year: Congress, and its affiliated agencies.

For the first time in history, the whole of the rest of the government has been operating under a "continuing resolution" of Congress, which runs out on Nov. 20, an Office of Management and Budget spokesman said yesterday.

For some programs, the continuing resolution allows spending at the same rate as in 1981. For others, it means spending according to the appropriations voted by the House, but not yet by the Senate. For Housing and Urban Development programs -- covered by the one appropriations bill that had passed a House-Senate conference at the start of the fiscal year--the continuing resolution funds spending at the conference report level.

This is complicated enough. However, the White House has now made it even more so. It has ordered non-defense agencies to spend, not at the level authorized by the continuing resolution, but at the rate requested by President Reagan in his latest budget-cutting proposals, whenever this is lower. In many cases it is much lower.

This is the latest in a series of administration initiatives that have revolutionized the budget process this year. Its aggressive use of reconciliation earlier this year to push through unprecedented budget cuts is a major reason for the delay in enacting the regular appropriations bills that provide the actual funds for government spending.

The president's search for still more budget cuts, announced only days before the new fiscal year began, stalled things further. But OMB officials decided to use the delay to their advantage by holding spending down to the president's requests while Congress deliberates.

To make this legal, OMB will send hundreds of deferral notices up to Capitol Hill in the next few days, informing Congress that the president does not intend to spend all the money appropriated under the continuing resolution. This may revive memories for some of the bitter fights over government spending under President Nixon.

However, the White House is acting within the limits laid down in the Impoundment Act of 1974 to the president's power to impound, or not spend, money appropriated by Congress. This allows the president to defer or rescind appropriated funds, provided that Congress agrees.

Rescissions, which are permanent, must be approved by both houses of Congress within 45 days of being proposed. But deferrals, which in theory merely postpone spending, stand unless overturned by an act of one house or the other within 30 days.

The administration hopes that as the House and Senate struggle to finish the permanent appropriations bills and to find new cuts of the size the president has called for, they will not be able to find time to pass still more legislation to overturn the deferrals.

Meanwhile there are some strange anomalies.

* Defense spending, which Reagan wants to increase, will be funded at 1981 levels. Budget officials may not mind this involuntary saving, but Defense Secretary Caspar W. Weinberger and the president may.

* Foreign aid and funding for the District of Columbia are also lower under the continuing resolution than they would be under the president's proposals.

* The Office of Policy Development in the White House has been given no money at all under the continuing resolution. When presidential adviser Martin Anderson turned down an invitation to testify before the relevant House committee last spring, the committee authorized no money for his office. Since this has now been incorporated into the continuing resolution, technically the office has no money.

But a budget spokesman said yesterday that the administration has decided just to go ahead and give out the money anyway on the grounds that Congress "didn't mean it."

Most observers of this budgetary quagmire agree that a new continuing resolution will be needed for at least some parts of the government when the present one runs out next month.

A budget spokesman has emphasized that the administration has yet to decide whether to send up still more deferrals. However, some senior administration officials believe that the deferral weapon can be used to hold down spending for as long as Congress goes on funding the government on continuing resolutions--provided only that it stops well before the end of the fiscal year, when a deferral automatically becomes a rescission.