Well, you can format the column in R so that it is left-padded with zeros, but the column type will then be character, which will be inconvenient if you want to do math with the column. In this example, I manually construct the data frame but you would import it with read_excel() instead.
DF <- tibble::tibble(Number = c(1, 12, 123, 1234, 12345))
DF$Number = formatC(DF$Number, width = 5, flag = "0", format = "d")
DF
# A tibble: 5 x 1
Number
<chr>
1 00001
2 00012
3 00123
4 01234
5 12345