Usually direct object will be found by putting question "by whom" and indirect object by "what". Is this true?

No, that's not correct. The direct object is acted upon; in your sentence the direct object is "rupee." "Rupee" is what was given.

"Him" is the indirect object. The indirect object is the person (or thing) to/for whom the action happened. The indirect object never has "to" or "for."

I sent her a letter. Direct object: letter. Indirect object: her.

I sent a letter to her. Direct object: letter. No indirect object.

In "I give him two rupee," 'two rupee' is the direct object, and 'him' is the indirect object. The Direct Object can be found by asking what or whom. Give what? two rupee.

Once you've found the direct object, ask who or what received it to find the indirect object.

"I give two rupees to him" - 'two rupees' is the direct object, and 'him' is the indirect object.

I give two rupees (to) him.

The action was performed on the rupees.