These days, it becomes a serious problem(the fact) that some middle-aged men don't work diligently and still earn a lot money which is not worthy of their outputsnot proportional to their outputs, has become a serious problem.

I added the 'still' to place emphasis.
Changed the ordering to make it sound more natural.

Their employments (status?) are is protected by labor laws in Japan, so employers have difficulty in dismissing them.

Japanese companies have paidpay wages based on seniority.

"have paid" sounds like this phenomenon doesn't happen any more, but I'm assuming it still does.

They had suffered from low wages and hard work, and undesired transfer, undesired transfers, and worked long hours .

It doesn't make sense to 'suffer from hard work'

While they can't builtd careers enough to earn enough by themselves, raising their children cost a lot.

Japanese society has a dilemma over whether to prioritizinge productivity or to protecting the employment of parental generationcaregivers.

'generation' often refers to people who are within a certain age range today. For instance, "my parent's generation" might refer to people in their 50s today. In fact, there are names of different generations depending on when people are born. (https://www.thoughtco.com/names-of-generations-1435472)

In this case, I assume you mean all people who are parents, and especially those with young children.

These days, it has becomes a serious problem that some middle-aged men don't work diligently and earn a lot of money which is not worthy of their outputs.

Their employments ( status?) are is protected by labor laws in Japan, so employers have difficulty in dismissing them.

Looks kind of ugly with the formatting, so just repeating it here:
Their employment status is protected by labor laws in Japan, so employers have difficulty dismissing them

However, this problem can't be just be attributed to middle-aged men.

Japanese companies have paidpay wages based on seniority.

They had suffered from low wages and, hard work, and undesired transfers.

When listing things in English, use "and" only on the last item, and separate the rest with commas.

Eg: Apples, oranges, bananas and watermelon.

While they can't built careers enough to earn bymay be able to earn enough for themselves, raising their children also costs a lot.

I'm not sure what this sentence means. I corrected it to mean that their wages could be high enough to pay for their own lifestyles, but children would still be expensive. If that is not what you meant, please clarify, and I will try to correct it better, because I'm not sure how to change it right now.

Japanese society has a dilemma over whether to prioritizinge productivity or protecting the employment of the parental generation.