The Ministry of Culture on Monday barred visitors from clambering over the monuments.
But by late yesterday it had revised the order to let tourists ascend five of the largest pagodas -- in a field of more than 3,000 Buddhist structures.
"We would like to replace the statement about banning the climbing of pagodas with an amendment exempting five designated pagodas in Bagan," the ministry said on its Facebook page.
The sudden ban had surprised tour operators and prompted concern that their businesses would take a hit.
In its updated post the ministry stressed that the regulation was aimed at conserving the Buddhist ruins, many of which are crumbling and overgrown.
The statement also warned that safety was a concern, citing the case of an American tourist who was hospitalised earlier this week after falling from one of the pagodas.
"Bagan's ancient buildings have been there for many years and we are concerned about damaging the pagodas and the danger of hurting people," the ministry said.
Once considered an off-the-beaten-path destination for intrepid travellers, Bagan's popularity on the tourist circuit has surged since Myanmar opened up its borders in 2011 following decades of isolation under military rule.
Tourism has since taken off, with the number of foreign visitors doubling in the past five years.
Myanmar is eager to see Bagan listed as a UNESCO world heritage site.
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