It was announced last month that the fantasy drama would be returning for a 10-part fourth series in 2012.
Speaking to SFX about the reduced episode count, Murphy said: "It was brutally about money. Merlin is an expensive show... and what we are not prepared to do is cut its budget or production values. The BBC has had a really tough [financial] hit."
However, he added: "We are now discussing the fifth series with the BBC, and I think [the 2011 break] potentially preserves the programme for longer. There is [also] talk of specials [and other] ways we can fill in the gap, but these are tough times for British broadcasters."
The showrunner also hinted that the final episode of the show's third series would contain "three or four absolutely iconic moments".
"The last two are very special episodes because probably there are more crucial moments from the legend in them than in any other," he teased. "The changes that happen in [episodes] 12 and 13... set up the direction that series four is going in. You get a good glimpse of the future."
The third series of Merlin concludes this Saturday at 7.40pm on BBC One.