diff --git a/pkgs/development/libraries/gmp/6.x.nix b/pkgs/development/libraries/gmp/6.x.nix
index 9093073cecff4..7bcc31e4fe8d0 100644
--- a/pkgs/development/libraries/gmp/6.x.nix
+++ b/pkgs/development/libraries/gmp/6.x.nix
@@ -2,6 +2,7 @@
 , cxx ? !stdenv.hostPlatform.useAndroidPrebuilt && !stdenv.hostPlatform.isWasm
 , buildPackages
 , withStatic ? stdenv.hostPlatform.isStatic
+, autoreconfHook
 }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
@@ -29,7 +30,7 @@ let self = stdenv.mkDerivation rec {
   passthru.static = self.out;
 
   depsBuildBuild = [ buildPackages.stdenv.cc ];
-  nativeBuildInputs = [ m4 ];
+  nativeBuildInputs = [ m4 ] ++ lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [ autoreconfHook ];
 
   configureFlags = [
     "--with-pic"
diff --git a/pkgs/development/libraries/isl/generic.nix b/pkgs/development/libraries/isl/generic.nix
index eb6fe5f9cd69a..5a82fdfd6ab3e 100644
--- a/pkgs/development/libraries/isl/generic.nix
+++ b/pkgs/development/libraries/isl/generic.nix
@@ -6,6 +6,7 @@
 }:
 
 { lib, stdenv, fetchurl, gmp
+, autoreconfHook
 }:
 
 stdenv.mkDerivation {
@@ -17,6 +18,8 @@ stdenv.mkDerivation {
 
   inherit patches;
 
+  nativeBuildInputs = lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [ autoreconfHook ];
+
   buildInputs = [ gmp ];
 
   inherit configureFlags;
diff --git a/pkgs/development/libraries/libmpc/default.nix b/pkgs/development/libraries/libmpc/default.nix
index 2dede1f976d22..d4c575a194349 100644
--- a/pkgs/development/libraries/libmpc/default.nix
+++ b/pkgs/development/libraries/libmpc/default.nix
@@ -1,5 +1,6 @@
 { lib, stdenv, fetchurl
 , gmp, mpfr
+, fixPathToUsrBinFileInConfigureScript
 }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
@@ -16,7 +17,7 @@ stdenv.mkDerivation rec {
     sha256 = "0n846hqfqvmsmim7qdlms0qr86f1hck19p12nq3g3z2x74n3sl0p";
   };
 
-  buildInputs = [ gmp mpfr ];
+  buildInputs = [ gmp mpfr ] ++ lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [ fixPathToUsrBinFileInConfigureScript ];
 
   doCheck = true; # not cross;
 
diff --git a/pkgs/development/libraries/mpfr/default.nix b/pkgs/development/libraries/mpfr/default.nix
index fc7eeeab94206..88a3bda8a8f01 100644
--- a/pkgs/development/libraries/mpfr/default.nix
+++ b/pkgs/development/libraries/mpfr/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, gmp }:
+{ lib, stdenv, fetchurl, gmp, fixPathToUsrBinFileInConfigureScript }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
 # cannot use fetchpatch! All mutable patches (generated by GitHub or
@@ -22,6 +22,9 @@ stdenv.mkDerivation rec {
   # mpfr.h requires gmp.h
   propagatedBuildInputs = [ gmp ];
 
+  # autoreconf with latest autotools will break mpfr
+  nativeBuildInputs = lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [ fixPathToUsrBinFileInConfigureScript ];
+
   configureFlags =
     lib.optional stdenv.hostPlatform.isSunOS "--disable-thread-safe" ++
     lib.optional stdenv.hostPlatform.is64bit "--with-pic";
diff --git a/pkgs/development/libraries/pcre/default.nix b/pkgs/development/libraries/pcre/default.nix
index 5fc8d496ba914..d8204f7a79620 100644
--- a/pkgs/development/libraries/pcre/default.nix
+++ b/pkgs/development/libraries/pcre/default.nix
@@ -1,5 +1,6 @@
 { lib, stdenv, fetchurl
 , pcre, windows ? null
+, autoreconfHook
 , variant ? null
 }:
 
@@ -20,6 +21,8 @@ stdenv.mkDerivation rec {
 
   outputs = [ "bin" "dev" "out" "doc" "man" ];
 
+  nativeBuildInputs = lib.optionals (stdenv.hostPlatform != stdenv.buildPlatform) [ autoreconfHook ];
+
   # Disable jit on Apple Silicon, https://github.com/zherczeg/sljit/issues/51
   configureFlags = optional (!stdenv.hostPlatform.isRiscV && !(stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64)) "--enable-jit" ++ [
     "--enable-unicode-properties"
diff --git a/pkgs/development/tools/misc/libtool/libtool2.nix b/pkgs/development/tools/misc/libtool/libtool2.nix
index 44e4c8665c839..109bdd704088f 100644
--- a/pkgs/development/tools/misc/libtool/libtool2.nix
+++ b/pkgs/development/tools/misc/libtool/libtool2.nix
@@ -1,4 +1,5 @@
 { lib, stdenv, fetchurl, fetchpatch, autoconf, automake, m4, perl, help2man
+, buildPackages
 }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
@@ -36,6 +37,25 @@ stdenv.mkDerivation rec {
     popd
   '';
 
+  # When detecting the `LD` (linker) command and flags for cross
+  # compiling, libtool.m4 expects to be able to use "/usr/bin/file" to
+  # detect host details like ABI and linker flags.  Unfortunately this
+  # detection code hardwires the path to /usr/bin/file, which is
+  # inaccessible for sandboxed builds.  This causes the `LD` flag to
+  # be detected incorrectly when cross-compiling to the following
+  # hostPlatforms: {x86_64, powerpc, s390, sparc, mips64*}-linux,
+  # x86_64-kfreebsd, *-solaris, *-irix, and *-hpux.
+  #
+  # This substitution is performed only for cross-compilation in order
+  # to avoid a mass-rebuild.  A separate PR will be submitted to
+  # staging, not to be merged until after nixpkgs-22.05 branch-off,
+  # which deletes this conditional and this comment.
+  #
+  preBuild = if stdenv.buildPlatform == stdenv.targetPlatform
+             then null
+             else ''substituteInPlace m4/libtool.m4 \
+                    --replace "/usr/bin/file" "${buildPackages.file}/bin/file"'';
+
   nativeBuildInputs = [ perl help2man m4 ] ++ [ autoconf automake ];
   propagatedBuildInputs = [ m4 ];
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 5d52bf43efcb7..38f30f5a0f8f8 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -179,6 +179,17 @@ with pkgs;
       }
     '');
 
+  # libtool.m4 invokes "/usr/bin/file", and is vendored into many ./configure scripts
+  fixPathToUsrBinFileInConfigureScript = makeSetupHook {}
+    (writeScript "fix-path-to-user-bin-file.sh" ''
+      postUnpackHooks+=(_fixPathToUserBinFile)
+      _fixPathToUserBinFile() {
+        if [ -e $sourceRoot/configure ]; then
+          substituteInPlace $sourceRoot/configure --replace /usr/bin/file ${buildPackages.file}/bin/file
+        fi
+      }
+    '');
+
   addOpenGLRunpath = callPackage ../build-support/add-opengl-runpath { };
 
   quickemu = callPackage ../development/quickemu { };