Japanese Visa Question

Only the immigration people have any idea about the visa approval process.

To answer your questions:
It will be a fresh application, and this time based on an internship with your expenses taken care of. You will have to disclose your previous unsuccessful application, and they will take that into account.
I'd have thought pretty good, but you need to ensure you submit all ducumentary evidence required, esp the full details of internship - what it covers, who pays for it, its duration etc from the uni itself. Usually unis are used to supporting visa applications and know what sort of documents you require. Ask them to send you ASAP. Do remember that you still need to pay for other things while you are in Japan, such as travels, incidentals, entertainment etc, so make sure you can account for it (e.g. bank statements).
Having said that, at the end of the day it's up to the consulate to decide whether to grant you a visa - all you can do is to comply fully with their requirements, with correct documents and so on. I wouldn't have thought using a visa agent would make much of a difference, apart from paying their considerable fees. But do go through your application form carefully with someone you trust, to correct any ambiguities or omissions.

@Alec:Thanks for your considerable reply.

I want to say that this time the university will be releasing official documents regarding all this stuff,including who will be paying for my accommodation expenses.

I will have to pay for the food,travel expenses myself.But I don't have a faintest idea of how much balance should I show them in bank account.(this is most probably the reason I got my previous application rejected.)

Thanx

It's difficult to lay down the precise amount you'll need every day, but as a rough guess, a student should be able to manage on around 3,000 yen a day on food and travels, maybe less if your commute isn't too long. Reckon around 500 yen for lunch, 1000 yen for dinner (eating out, cooking yourself), 500 yen for travels and 1000 yen for incidentals like books, stationery, toiletries etc. You can cut down on costs by using 100 yen shops and library for books.

@Alec:Tahnks for the reply.Please explain about the 100 yen shops.What do they sell.

I need to know about the cost-cutting measures I can take to reduce my daily expenses there in Japan.

Keeping my fingers crossed for the visa.

Thanks.

Don't you have it in India? A bargain shop selling household items, toiletries, stationery, even non-perishable food for a low set price. In Japan most items are priced 100 yen plus 5% tax. There is a pound shop in UK, euro shop in Eurozon and dollar store in US.

There are "JUSCO $10 Plazas" in Hong Kong too.

Your visa situation may be more complicated if you give "internship" as a reason for the visit instead of tourism. In the USA, the sponsoring institution for an internship or for a foreign student has to submit appropriate documentation and the visa falls into a special category. You should have the faculty member who is sponsoring you in Japan find out from the university what, if any, supporting documents are required for you.

Four times over the years I've used an "Application for Certificate of Eligibility." To return to your original question, it would be a different kind of application this time because you are in a different category. Instead of checking the box that says "Student" you could now check the "Researcher" box, a stronger category. Likely the better approach is to stress the research aspect rather than the internship aspect.
The Japanese University I go to as a visiting professor sends me this "Application for Certificate of Eligibility," which I fill out and return to the University. Then they apply on my behalf to an immigration office in Japan for the Eligibility Certificate, which, once completed, they forward to me. I use that Certificate in Canada to apply at the Embassy or nearest Japanese Consulate General in Canada for the visa itself. The visa stamp is given the next day.
I'm not sure if this is the procedure you followed last time--or will this time. But it puts the onus somewhat on the sponsoring institution to apply as your proxy.
U of Tokyo is big enough and prestigious enough, with lots of international students, to have an office that can lead you through his process. Ask them to assist you.

Thanks a lot for the replies from anyone.

@WillJame:Thanks a lot.But I am not getting any pay from the University.They are bearing my accommodation only.Will this process be valid in this case too.

To Everyone on the forum:
I need to know about the cost-cutting measures I can take to reduce my daily expenses there in Japan in case I get the visa.

Thanx.

Visit_it, you are straying far from your own original topic, the question of your visa. The issue of living cheaply in Japan is for another thread, once you have the visa matter sorted out.
As I suspected, the University of Tokyo website has the answers to the kinds of questions you are asking here. They also have a pdf file on their visa consulting service that has information about the application for the Certificate of Eligibility I referred to, including the proxy application process. See http://dir.u-tokyo.ac.jp/en/kokusai/visa.html
I see there is also scholarship information for research students like you, as well as information about part-time employment, and living costs. You need to hunt though the detailed information that Todai has provided to help their international students rather than seeking answers to general questions on this forum. Good luck with your studies in Japan.