SYDNEY, Nov 29 (Reuters) - Rain in Australia's key southeast grain growing region is boosting the country's expected wheat crop but could delay the harvest by up to five weeks and threatens crop quality, industry experts said on Monday.

The wheat harvest is already running up to five weeks late in parts of southeast Australia and persistent rain is slowing progress, GrainCorp Ltd , the country's largest grain handler said on Monday.

"It is still early days but in some areas ... they may still be going until February," said GrainCorp spokesman David Ginns.

Australia's weather bureau is forecasting further rain throughout this week across the states of Queensland, New South Wales and Victoria as well as for parts of South Australia.

"The forecast this week is very poor for east coast harvest progress and grain quality," said Luke Mathews, an agricultural commodities strategist with Commonwealth Bank of Australia, in a market report.

The rain, attributed to a La Nina weather event, is boosting yields, leading to forecasts of up to 25.5 million tonnes, nearly 18 percent above last year's level.

Wet weather has also raised concerns that crop quality will be affected due to crops sprouting while yields have been boosted at the expense of protein levels.

Grades of grain received into GrainCorp's handling system in Queensland were mixed, the firm said in a harvest report, adding that 60 percent of the state's harvest was complete.

In northern New South Wales, GrainCorp, said the harvest was 45 percent complete although receivals in western areas were being disrupted up by rain.

Quality was holding up well across northern New South Wales, the firm said, adding that it was not seeing usually high levels of feed wheat delivered into its system.

Queensland and northern New South Wales produce most of Australia's high protein wheat.

In a normal year around two million tonnes of top quality wheat are harvested but this year as little as 250,000 tonnes might be reaped, according to some estimates.

"May be GrainCorp is not seeing the levels of feed wheat or downgraded wheat that is about simply because growers may prefer to hold it on-farm or deliver it directly to the domestic market," said Gavin Warburton, an analyst at Australian Crop Forecasters (ACF).

"It is not a good scenario, the continuation of the rains in terms of getting a good crop off," he said.

Potential shortages of high protein Australian Prime Hard (APH) wheat have boosted premiums for APH grades over Australian Premium White (APW) milling grade wheat in the domestic market to 15-years.

The harvest delays have also led to an inversion in eastern Australian milling wheat futures prices, with milling wheat for January delivery trading on Monday at A$256 ($246.41) per tonne versus A$255 per tonne for March .

Western Australian wheat is also trading at a substantial premium to eastern state prices, reflecting a shortages due to prolonged dryness during the growing season.

ACF estimates Western Australia, usually the country's top grain exporting state, could harvest as little as 3.5 million tonnes compared with 8.2 million tonnes in 2009/10.

Western Australian wheat futures for January delivery were trading at A$288 per tonne on Monday, a 13 percent premium to the east coast contract.