We'll never know the number shot down by flak or other means. If the aircraft was lost, many times even the side destroying it really doesn't know what killed it.
As far as losses, this is about all I can find that I feel is in the ball park:
"according to the Luftwaffe's own records" 2,093 aircraft destroyed to all causes, from June 22 to December 6 1941, on the Eastern front (758 bombers, 568 fighters, 170 dive-bombers, 330 reconnaissance, and 267 miscellaneous), another 1,362 (including 473 bombers and 413 fighters) damaged (again, to all causes)"
Source: Ellis, John (1993). World War II - A statistical survey. Facts on File
The Luftwaffe later reported, for the time period Sept 1939 to Dec, 1944 the following:
- 40% of all losses were accidents, landing mistakes, or pilot errors)
- 15% were unknown (this includes airbases being over run)
- 45% were combat losses
-- 30 % pts were air to air
-- 15 % pts were other (read flak)
However, this includes the massive losses over Germany during the strategic bombing campaign, so not sure how accurate this would apply to the East front.
Next, for specific time periods that the Luftwaffe did samples, it came up with very different numbers that you simply can't reconcile to either the total it reported above OR to each other OR to operational reports (the Germans weren't the only one's that had this problems; so did the Americans, British and Japanese so it wasn't an easy task).
And the East front samples indicated a higher loss rate due to ground fire (literally bullets from MGs, rifles, etc.. that suffered on other fronts, both for down and damaged aircraft).
As for cause of Soviet losses, I simply haven't found anything that I feel I can trust. Doesn't mean that its not out there, just I don't feel really comfortable with the numbers I've seen.
Wish I could provide a more "definite" answer, but this is the best I have seen. And I think the Germans "guesstimate" a lot of their estimates based on incomplete information. But I doubt anyone has been guesstimates.