I hate to break it to you, devokeuk, but unless the agency/company has agreed to pay the taxes for you (highly unlikely) the taxes due are most certainly your responsibility....either way.
And, airline companies use an agency for a reason, among them is the ability of sheding folks without recourse for any reason whatsoever, and oftentimes sign an exclusive with one agency, so going 'directly' to the specific airline is generally not possible.
So, what we have is...
keep your nose clean, and follow company and agency procedures and, most important...don't believe anything without getting it firmly in writing, and even then it can be changed by the airline company at their whim.
The agency works for the airline, so they have no leverage whatsoever and in most cases, will not go to bat for you if difficulties develop.
Not being negative you understand...just realistic.
Better you should know now rather than find out the hard way.