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Last part of the statement is incorrect that you can’t see the status of your application because it’s first time.

Secondly, once the work pass applied online, it takes a day or two to update EPOnline site. So, using your passport number and DOB you are able to check the status of application. I feel the agent didn’t apply but instead telling the truth, they are telling lie to you. Good luck

It sounds like a typical dishonest agent.
Ask them for the FIN or application reference number (which they get from MoM soon after the application is submitted). If they do not want to give it to you, forget about it and look for another employer. I hope you didn't pay this "agent" - only dishonest ones charge the job seeker!

Yes i have asked for my application number.but they denied to give me because that is the rule of them agency to do not share application number till they get approval.

And employer can apply manually

Then they are certainly faraudsters. There is bo legitimate reason to withhold the application number!
I am quite sure there is no application submittes - and probably also no job for you!