Quick version: it looks that way, but the filmmakers are being very coy.
In an interview with the NY Daily News published May 11, 2014, director Gareth Edwards says:
“As we were writing the film, the horrible events in Fukushima happened and we had to make the decision: Do we stay away from that or do we acknowledge that you’ve opened this Pandora’s box of nuclear power, and when it goes wrong, it really does go wrong?”
This is careful and kind of odd phrasing. Edwards is talking about incorporating elements of the Fukushima Daiichi nuclear disaster into the film, but then veers off mid-sentence into a big picture thing. My takeaway is that a Fukushima reference was considered.
In an interview with Scifi UK published May 16, Edwards says:
“When you list what makes a Godzilla movie two of those things that come up are radiation and Japan, and so once the events happened that were horrific for real in Japan, we had to be very careful and sensitive not to do something that would be considered insensitive to what happened there.
“Our film is not based on anything to do with Fukushima, it’s in a fictional city outside of Tokyo and happens 15 years ago, but that said it does deal with the genuine problem of around the world we have these nuclear power plants and we benefit from it."
This again is careful phrasing. It sounds like pains were taken to avoid a direct reference, but again Edwards acknowledges the correlation between his film and real world events.
I have to believe that with all this consideration going on, whether the Janjira scene was inspired by Fukushima or not, enough thinking went into it that by including the scene in the final film Edwards is conscious of what it evokes. In that sense, it is a reference.
According to Wikipedia, scriptwriting began in October 2010, five months before the March 11, 2011 earthquake and tsunami that compromised Fukushima. Rewrites continued through 2013. It's unclear when the scene was conceived or who wrote it, but evidence points to Frank Darabont, in this exchange on io9 in January 2013:
Are you looking to connect it to a different contemporary issue [than the atomic bomb]?
Frank Darabont: Yes I am, but I'm not going to give it away.
This statement certainly could be regarding Fukushima/Janjira.
Reviewers are quick to make the connection:
Godzilla's basic plot centers around the fallout, literal and metaphorical, from a Fukushima-like nuclear plant meltdown. (Ars Technica)
[Janjira is] a barely-disguised reference to the real-world Fukushima nuclear plant meltdown... (Times of India)
The movie opens with a disaster at a Japanese nuclear power reactor -- an obvious reference to the 2011 incident at the Fukushima facility. (HuffPo)
Of course, imagery of a collapsing nuclear plant are evocative of feelings about Fukushima, but it bears mention that no such collapse ever occurred: the meltdown was due to flooding from the tsunami caused by the 3/11 earthquake which compromised the plant's cooling system. The way destroyed city buildings tend to evoke memories of 9/11 regardless of context, anything relating to Japanese nuclear safety may appear to be a reference to the meltdown, but as of right now, evidence that Janjira is a reference to Fukushima is merely circumstantial, and possibly distorted by emotion.
Addendum: As of this writing Godzilla (2014) has only been in theaters for about a week and is not yet released in Japan. I expect a greater discussion of scenes like this once the whole world has a chance to react, and perhaps then the filmmakers will feel comfortable explicitly saying what influenced what. Maybe in the DVD commentary? I'll try to keep this answer updated.