Is it permissible to obtain a loan from the Jordan Islamic Bank to open a dairy factory, knowing that the bank takes annual profits at a rate of 6% on the amount, where the borrower purchases the equipment and submits its invoices to the bank so that the bank pays the merchant for them and adds its profits to the invoice?

The transaction mentioned is impermissible because it is an interest-based loan. The permissible form is Murabaha for the one who commands the purchase, where there is a non-binding promise from you to the bank to purchase a specific commodity. Then, the bank takes legitimate possession of it, and then sells it to you in defined installments. There is no harm in there being an increase in its price compared to its spot price.