The format of my excel data file is:
day value
01-01-2000 00:00:00 4
01-01-2000 00:01:00 3
01-01-2000 00:02:00 1
01-01-2000 00:
I think this is a more general solution, which relies on creating a sequence of all timestamps, using that as the basis for a new data frame, and then filling in your original values in that df where applicable.
# convert original `day` to POSIX
ts$day <- as.POSIXct(ts$day, format="%m-%d-%Y %H:%M:%S", tz="GMT")
# generate a sequence of all minutes in a day
minAsNumeric <- 946684860 + seq(0,60*60*24,by=60) # all minutes of your first day
minAsPOSIX <- as.POSIXct(minAsNumeric, origin="1970-01-01", tz="GMT") # convert those minutes to POSIX
# build complete dataframe
newdata <- as.data.frame(minAsPOSIX)
newdata$value <- ts$value[pmatch(newdata$minAsPOSIX, ts$day)] # fill in original `value`s where present
newdata$value[is.na(newdata$value)] <- 0 # replace NAs with 0