Is it permissible for an accountant to take his financial dues from an excess amount in the company's custody?

It is not permissible to take one's right in this manner. Rather, one must demand it from the company's management or inform them that it will be taken in lieu of the right, because taking it without their knowledge is a betrayal of trust. Allah the Almighty said: "Indeed, Allah commands you to render trusts to whom they are due," and He said: "O you who have believed, do not betray Allah and the Messenger or betray your trusts while you know [the consequence]." And the Prophet, peace be upon him, said: "Render the trust to the one who entrusted you, and do not betray the one who betrayed you."

As for securing one's right, this applies when it is denied and there is no other way to obtain it except through this method, which is a matter of scholarly disagreement. The moderate view distinguishes between cases where the reason for the right is evident—in which case the person who takes it is not accused of betrayal—and cases where it is hidden—in which case taking it is considered betrayal.