In her letter JK called the use of the cages - which are also used in Slovenia, Hungary and Slovakia - "torture" and the United Nations has also attacked the use of them in the past.
President Vaclav Klaus said he wondered if JK really knew that much about it or was responding to pictures she had seen.
A spokesperson for JK Rowling in Edinburgh said: "JK Rowling is very pleased to see that the issue seems to be getting the attention it deserves from the Czech government.
"She is continuing to speak to the people who are running the campaign against cage beds.
"She is keen to do whatever she can to help end this inhumane practice."