1- While it appears that Sweden and Italy have the same system in controlling X, our results indicated a lower quality of X in Sweden compared with Italy. We hypothesize that the low quality of X in Sweden may be due to a difference with the reporting system of M.
It reads more fluently if you include the 'that'
You are suggesting that there may be a difference. You have not stated what this difference actually is, that would then be referred to as 'the difference' = the specific/particular difference you have mentioned.
I think 'with the reporting system', as you have written, is better than 'in the reporting system', which is another possibility.
2- In Italy, K publicly disclose summary of all M. Contrary to that, the P does not publicly disclose the M to the public in Sweden. The ethics committee only informed the findings and names of companies involved to the P. In addition to that, our request from the organisation failed to provide any information.
This does not read well, and appears to have grammar mistakes, but is too obscure to correct. You would need to substitute some actual nouns for the letters, so, for one thing, we can see if the noun is singular or plural.