A Muslim should always be cautious with regard to the sources of his income. Unfortunately, the sources of Islam-compliant works have been diminishing due to the prevalence and domination of non-Islamic systems throughout the global market.
Responding to a question of this nature, Dr. Main Khalid Al-Qudah said:
Generally speaking, direct and explicit involvement in any prohibited business is also prohibited.
According to the description of your company’s core business, there is no such direct involvement in the business of the companies you represent or for whom you submit applications to the state – neither in permissible nor impermissible activities. Not all the companies whose applications you forward and process conduct prohibited business; it is just a few of them.
However, this does not necessarily mean that the work you do is purely halal, because your company facilitates these companies’ ability to do business, although indirectly. The greater the percentage of companies conducting haram business, the more doubtful and questionable your work will be.
For the time being, it is highly recommended that you give a portion of your salary to charity, in order to purify it (in addition to paying your obligatory zakah). If you could also find another job that does not require such processing for the companies in question, that would be much better.