I passed JPLT N5 exam with average score, should I be worried about MEXT examinations in Japaneese? As part of preparation for MEXT scholarship I had given JPLT N5 examinations (I know I will give seperate written examinations in Japanese and English as well for the Mext Scholarships) and I got average scores (~97/180) on it.

My major is in Computer Science with a Masters in Digital System's security and I plan for a PhD in Japan. So I wonder does by having an average score in JPLT N5 mean that I can have a low score in Japanese examination for MEXT?

What worries me is a failure for my application for being rejected, because of low Japanese level. Also, I wanted to know how does the English test affect my application as well (I am really confident on my English level.)? 

Also, should I focus on getting My Japanese on N3 Level before applying, as seen on this answer a good result in these examinations is a crutial part of a successful MEXT application. Though the answer is for an application through Indian Japanese embassy and not the one that is in Greece (I am a Greek native). If yes (bringing my Japanese in N3 level) I think I may not have as many chances due to time limitation (cap for research students is 35yrs old, and I am 29.)
I think the evaluation varies a bit from country to country but in my case (from Tunisia in 2008 for doing Master degree), Japanese language ability was absolutely not required. We passed the English and Japanese test, but I left most of the Japanese test sheet blank, and my friend (who also got the scholarship) did not know any Japanese except for some words (konnichi wa, arigatou, ...).
The embassy then chose the topmost scorers from the English test and invited us to the interview at the Embassy. During the interview, there were many questions about our capacity to live in Japan and to adapt to life there (because many people get the scholarship but don't acclimatize well and drop off in 6 months or a year). Language ability was a bonus but not an absolute requirement because we spend the entire first year learning Japanese at the university you get.
This was also the case for many of my friends that I met in Japan: many of them had no japanese skills when they got the scholarship.
So unless things changed a lot in the last years, your japanese language ability should not have too much of a bearing on your application, and the fact that you got the N5 already is a boost!
Good luck for it!