Dependent visa cancellation within one month

Questions:
1. Who paid for your dependent pass? You or your wife's company?
2. Who requested the penalty? Company or immigration?

I am not sure about immigration penalty for not completing at least 2 months of dependent pass.

But, if your wife's company paid for your dependent pass and it is the company who requested the penalty, it is quite reasonable for them to do that.
They spent time, money and effort to get you a dependent pass but now suddenly you want to cancel. So, maybe they want to get compensation for their effort.

1) My wife paid for the dependent paas not her company morevoer they have taken 1000rm extra for dependent visa saying that its agent fees.

2) The penalty is requested from my wife's organisation.

Usually, agents will charge very high price.
Some companies who process the visa by themselves will not have this issue.

I'd tried to check on the internet about penalty for not utilizing dependant pass but cannot find any info.

Check your visa sticker whether the place of issue is ESC. If yes, you may try to check with MyXpats on the penalty issue: https://esd.imi.gov.my/portal/about-us/contact-us/
MyXpats are fast in giving response, even replying emails.

But, try to ask in objective manner, checking whether the penalty is real exist and if yes, whether it is legal to do so.

Thank you for the help really appreciated.

But the place of issue on my dependent visa is UNIT IMIGRESEN PAS PENGGAJLAN DI MDEC.

The immigration rule (whether penalty exist or not) shall apply to all the branches.

Or, you may check with  MDEC immigration office
https://ibb.co/27shP45

But i never deal with MDEC immigration office.
Not really sure about their response speed for inquiries.