Dr Mudawi was arrested on Sunday afternoon just hours before he was due to board a flight en route to Ireland.
He was selected for the award because of his courageous and inspiring work for human rights in Sudan, including Darfur, which led to him being twice imprisoned in the last year.
Reports from Sudan say that his passport has been confiscated and that he has been charged under Articles 53 and 57 of the 1991 Criminal Act for "espionage against the country" and "photographing military areas".
Article 53 carries a potential death penalty or life in prison.
Front Line spoke to Dr Mudawi in prison earlier today and he sent the following message to the awards ceremony:
"Thank you for your support. I will continue the effort in Sudan to bring democracy and rule of law so that people's rights are respected. I thank Front Line for exerting pressure to defend human rights defenders and for supporting them. I really appreciate it. I exhort people to support Front Line in this work. I also want to thank the Irish Government for their efforts and ask them to continue. I am grateful for the award and honoured by the presence of the President of Ireland."