House prices unexpectedly fell 0.6% in April compared to the month earlier, having been expected to add another 0.1% as was seen in March.
On an annual and non-seasonally adjusted basis, price growth slowed to 3.4% from 3.9% a month ago, while an improvement to 4.2% had been expected.
Nationwide's chief economist, Robert Gardner, said this softening in house price growth "was to be expected, given the changes to stamp duty at the start of the month".
"Early indications suggest there was a significant jump in transactions in March, with buyers bringing forward their purchases to avoid additional tax obligations."
He expects the housing market to "remain a little soft in the coming months, following the pattern typically observed following the end of stamp duty holidays".
"Nevertheless, activity is likely to pick up steadily as summer progresses, despite wider economic uncertainties in the global economy, since underlying conditions for potential home buyers in the UK remain supportive."
Alice Haine, analyst at Bestinvest, agreed that the softer market was not a big surprise, not only reflecting the increase in stamp duty bills from April 1, along with the traditional Spring surge in listings, which can help to keep a lid on prices.
"A spike in the number of homes for sale is typical for this time of year as buyers look to take advantage of improving temperatures and longer daylight hours to showcase their interiors and gardens. While more homes for sale gives buyers greater choice, the uptick in listings is not being met by a similar uplift in demand."
The recent emergence of a mini mortgage price war between lenders has provided hope for the market though.