There are hints in the movie; when Alfred calls Harriet to ask her when she's coming back to the office, she doesn't answer and so he goes to her flat where she accuses him of having Asperger syndrome, which is a kind of autism:
Harriet: Look, I'm not... I'm not coming into work, all right, because I need to stay here. I need to be here in case there's news. So, actually, anyone with a shred of understanding, or humanity, or simple feeling, who, frankly, wasn't suffering from some kind of Asperger's, would know that the last thing that I need is your bullying little phone call asking me to come into work so that you can update me on fish... You want to fill me in on fishing. Well, Dr. Jones, you can take your work and you can shove it up your unfeeling arse.
Fred: I didn't come here to talk to you about work.
Harriet: Then why are you here?
Fred: I made you a sandwich.
And a few minutes later:
Harriet: I'm so sorry about what I said before. That is just unforgivable.
Fred: The great thing about people with Asperger's is it's very difficult to hurt their feelings. So it's all right, you can say whatever you like.
It's not absolute confirmation though, because he could just be sarcastically throwing it back at her (though I don't think so). So I did a little more digging:
According to the TVTropes page, Dr. Alfred Jones suffers from Ambiguous Disorder (emphasis mine):
This character's behaviour is so bizarrely outside the norm that Real Life psychologists would be scrambling for the diagnostic manual to try to figure out what to diagnose them with. It's way beyond mere ordinary quirkiness. No reasons are given for the strange behaviour. No specific diagnosis is ever mentioned in the story. In fact, any resemblance to any real disorder is likely accidental; the character's symptoms are exactly those symptoms the writer wants them to have. It is a case of Ambiguous Disorder.
However, I found this interview with the scriptwriter, Simon Beaufoy in which he states that Fred is "on the spectrum":
Q: Now it’s been over a year since I read the script, but if I remember correctly, Fred, the main character, is a rather prickly sort. When you write characters that are in danger of coming off as unsympathetic to the audience, are you conscious of that? And if so, what do you do to endear them to the audience more so that they root for them?
Beaufoy: Fred is not at all likeable for a good deal of the script. That's the point, really. But we see the possibility of a kind, funny person trapped inside a dull shell, too scared to be the person he could be. And we want him to succeed. Many years ago, Alfred Uhry read a treatment of mine for another film and had only one question: "do we like him?" I answered with all sorts of clever stuff about how he was a complicated, layered person at a crossroads in his life, blah blah and he just repeated the question: "do we like him?" It took a long time to really understand the simple and perfect beauty of that question. It really is that simple and that complicated. Do we like Fred? He's spectrum autistic, rude, humourless, apparently passionless. However, in a moment of weakness (as far as he's concerned) he reveals his care and love for Harriet by making her a duck sandwich. And in that moment, ridiculously, we like him. After that, anything's possible.
That doesn't make it very clear though, but I found another interview with him in which the interviewer states that Beaufoy added this character trait in and it was not in the novel:
By reducing Jones’ age and giving him Asperger’s syndrome, an autism spectrum disorder, Beaufoy added a quirky flair to the character that gives the audience a completely different experience in watching a man overcome himself to achieve happiness.
It's not very concisely written, but if it really is an interview as it claims, I'd assume Beaufoy would correct him if it was in the novel (and I've seen no evidence that it is).
Furthermore, Wikipedia has it in the films about autism category.