1. Since both of you are Indian by origin then apply for registration of marriage through Indian embassy as it can register marriage under Foreign Marriage Registration Act which is considered as registration under Special Marriage Act.

2. Do not go for HK marriage certificate if both of you are still Indian passport holder and Hindu by religion.

3. Else  come to India, perform the marriage as per Hindu rites and customs and then register the marriage under Hindu Marriage Act. This whole process would not take more than a week and does not require much paper work.

If you are residents of japan you should get married in Japan and registeryour marriage with Indian embassy under provisions of foreign marriage act 

2) if you are getting married in Hong Kong then marriage should be registered with Indian embassy under provisions of foreign marriage act 

3) 

Required documents:

1. Completed application form for "Solemnization/Registration of marriage" with one passport size photo affixed in the box.
2. Fill in all the information correctly. Incomplete application will be returned without service.
3. Original and one copy of identification pages of the passports of all the five individuals.
4. Copy of Proof of address (utility bill, driver license or lease agreement).
5. Copy of valid Visa/Green Card for Indian citizens and for other citizens of Indian origin attach a copy of their OCI card/PIO card/Renunciation of Indian Citizenship Certificate (if applicable).
6. Notice of intended marriage (4 copies) (Form-I).
7. Declaration by prospective bride and bridegroom in duplicate (Form-II).
8. Sworn Affidavit by prospective bride and bridegroom in duplicate.
9. Four identical, passport size, recent, photographs each of prospective bride and bridegroom.
10. Fee $50 and $2 for ICWF.
11. Fee is to be paid by cashier’s check or money order drawn only in favor of "Consulate General of India". There should be a seperate cashier's check or money order for ICWF Fee. Cash payment is also accepted at the counter of the Consulate. Applicants are requested to come with exact change for efficient services.
12. Personal checks, Debit cards and Credit cards are not accepted.
13. If application is being sent by post please sent a seperate $20/- cashier’s check or money order fee for return mail. No prepaid envelopes are accepted.

See it has to be registered under Foreigners marriage act under jurisdictional embassy.

Documents required are

1. Completed application form for "Solemnization/Registration of marriage" with one passport size photo affixed in the box.
2. Marriage certificate.
3. Original and one copy of identification pages of the passports of all the five individuals inciuding three witness.
4. Copy of Proof of address (utility bill, driver license or lease agreement).
5. Copy of valid Visa/Green Card for Indian citizens and for other citizens of Indian origin attach a copy of their OCI card/PIO card/Renunciation of Indian Citizenship Certificate (if applicable).

Please note that the Indian Embassy is not the registrar of marriages you can register your marriage locally And Get It authenticated by the embassy and that will be required to get your marriage registered in India for an Indian national registration of marriage in India is mandatory to claim any matrimonial benefit in India

Please check with indian consulate and/or the Hong Kong Marriage Registration Office before hand to find out which documents you have to provide.

1. Your Indian national fiancee  can marry before  the Indian consulate at Japan  or KH based on Foreign Marriage Act.

2. It will be valid in India also.

3. Marriage registered at HK and notarised by the Indian Consulate at HK will not be considered as registered in India but simply notarised by Indian consulate.

Yes it is to be done in Embassy of HK for jurisdiction purpose

The marriage performed in a foreign country cannot be registered as per Indian law in any Embassy.

They have to register the same before concerned marriage registrar in India under special marriage act.

Alternately you can get your marriage solemnised in Indian Embassy and register the same under special marriage act.