diff --git a/NEWS.md b/NEWS.md
index 23e8d5c873..c7f85ced85 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -24,6 +24,8 @@
 
 3. Vignettes are now built using `litedown` instead of `knitr`, [#6394](https://github.com/Rdatatable/data.table/issues/6394). Thanks @jangorecki for the suggestion and @ben-schwen and @aitap for the implementation.
 
+4. `fread` now prints a message by default when creating one or more integer64 columns, warning that this type sometimes give unexpected results like in case of as.matrix(). The message can be suppressed with the new argument `no.integer64.message=TRUE`. To avoid integer64 columns, we can use options(datatable.integer64='numeric'). Thanks to @stefanfritsch, @mattdowle for the suggestion. [#3611](https://github.com/Rdatatable/data.table/issues/3611)
+
 ### BUG FIXES
 
 1. `fread()` with `skip=0` and `(header=TRUE|FALSE)` no longer skips the first row when it has fewer fields than subsequent rows, [#7463](https://github.com/Rdatatable/data.table/issues/7463). Thanks @emayerhofer for the report and @ben-schwen for the fix.
diff --git a/R/fread.R b/R/fread.R
index 2f397b78e1..d89c784606 100644
--- a/R/fread.R
+++ b/R/fread.R
@@ -7,7 +7,8 @@ showProgress=getOption("datatable.showProgress",interactive()), data.table=getOp
 nThread=getDTthreads(verbose), logical01=getOption("datatable.logical01",FALSE),
 logicalYN=getOption("datatable.logicalYN", FALSE),
 keepLeadingZeros=getOption("datatable.keepLeadingZeros",FALSE),
-yaml=FALSE, tmpdir=tempdir(), tz="UTC")
+yaml=FALSE, tmpdir=tempdir(), tz="UTC", no.integer64.message=FALSE
+)
 {
   if (missing(input)+is.null(file)+is.null(text)+is.null(cmd) < 3L) stopf("Used more than one of the arguments input=, file=, text= and cmd=.")
   input_has_vars = length(all.vars(substitute(input)))>0L  # see news for v1.11.6
@@ -261,6 +262,7 @@ yaml=FALSE, tmpdir=tempdir(), tz="UTC")
     if (identical(tt,"") || is_utc(tt)) # empty TZ env variable ("") means UTC in C library, unlike R; _unset_ TZ means local
       tz="UTC"
   }
+
   ans = .Call(CfreadR,input,identical(input,file),sep,dec,quote,header,nrows,skip,na.strings,strip.white,blank.lines.skip,comment.char,
               fill,showProgress,nThread,verbose,warnings2errors,logical01,logicalYN,select,drop,colClasses,integer64,encoding,keepLeadingZeros,tz=="UTC")
   if (!length(ans)) return(null.data.table())  # test 1743.308 drops all columns
@@ -268,6 +270,18 @@ yaml=FALSE, tmpdir=tempdir(), tz="UTC")
   require_bit64_if_needed(ans)
   setattr(ans,"row.names",.set_row_names(nr))
 
+  # integer64 message on create - instead of warning
+  if (!isTRUE(no.integer64.message) &&
+      identical(integer64, "integer64") &&
+      any(vapply(ans, inherits, logical(1L), what = "integer64"))) {
+    message(
+      "fread: Creating one or more integer64 columns. 
+      See ?fread and ?bit64::integer64.
+      To suppress this message, use no.integer64.message=TRUE.
+      To avoid integer64 columns, use options(datatable.integer64='numeric')."
+    )
+  }
+
   if (isTRUE(data.table)) {
     setattr(ans, "class", c("data.table", "data.frame"))
     setalloccol(ans)
diff --git a/inst/tests/tests.Rraw b/inst/tests/tests.Rraw
index fcf78e9f36..4764f848d8 100644
--- a/inst/tests/tests.Rraw
+++ b/inst/tests/tests.Rraw
@@ -21978,3 +21978,12 @@ local({
   test(2357.1, fread(f), DT)
   test(2357.2, fread(paste0("file://", f)), DT)
 })
+#3611 fread integer64 message
+test(2358.1,
+  suppressMessages(fread("a\n1\n2\n", colClasses = "integer64")),
+  data.table(a = as.integer64(c(1,2)))
+)
+test(2358.2,
+  suppressMessages(fread("a\n1\n2\n", colClasses = "integer64", no.integer64.message = TRUE)),
+  data.table(a = as.integer64(c(1,2)))
+)
diff --git a/man/fread.Rd b/man/fread.Rd
index 40d2cfcc90..c79331a3bc 100644
--- a/man/fread.Rd
+++ b/man/fread.Rd
@@ -25,7 +25,8 @@ nThread=getDTthreads(verbose),
 logical01=getOption("datatable.logical01", FALSE),
 logicalYN=getOption("datatable.logicalYN", FALSE),
 keepLeadingZeros = getOption("datatable.keepLeadingZeros", FALSE),
-yaml=FALSE, tmpdir=tempdir(), tz="UTC"
+yaml=FALSE, tmpdir=tempdir(), tz="UTC",
+no.integer64.message=FALSE
 )
 }
 \arguments{