Quoting from Ministry of Foreign Affairs- FAQ
Please check whether you are eligible for Transit Visa / Pass or not. The following are conditions for the said visa / pass:
(i) Indian visitor(s) who enter / depart to / from the country from Kuala Lumpur International Airport (KLIA) and Low Cost Carrier Terminal (LCCT) only;
(ii) Visitor must possess a valid visa (Single Entry / Multiple Entry) from the destination country (only Australia, U.S.A., China, Japan, South Korea, New Zealand and Taiwan);
(iii) Visitor must possess a valid passport / travel document with an expiry date of not less than 6 months on the date of visit;
(iv) Visitor is not listed among those barred from entering Malaysia;
(v) Visitor must be in possession of a confirmed ticket to a third country;
(vi) Visitor must be able to finance his/her stay in Malaysia;
(vii) Visitor MUST visit the country in group (package tour) and the trip is either a packaged tour in Malaysia or in the destination country; and
We are a group of 3. 2 of us will hold a tourist visa from the destination country(Japan) and one with a residence card. Are we eligible for the Transit Pass?
However What does the point (vii) mean group (package tour)? should this also contain accommodation (Hotel). My plan was to book an accommodation myself and visit places on my own?
Also point (vi) how are we suppose to prove our finances? As it simply states must be able to finance.
Edit: I am planning to book a ticket in such a way that I can spend 24 hrs in KUL and fly to Tokyo. A night in the hotel and day to visit places. I will be booking my tickets in Malaysia Airlines