Its seems like i was passing wrong parm values to the configure scripts, so it always considered as native build rather than the cross build. I made some changes to the parms and it was able to generate the make file for cross build

./configure -Dsysroot=/opt/qnx6 -Dcc=arm-unknown-nto-qnx6.6.0eabi-gcc --target-tools-prefix=arm-unknown-nto-qnx6.6.0eabi- --target=arm-unknown-nto-qnx6.6.0eabi --host=arm-unknown-nto-qnx6.6.0eabi -Dprefix=$HOME/localperl

The make run fine for some time and end up having following error , where it says undefined references to certain functions

chmod 644 "PPPort.bs"
arm-unknown-nto-qnx6.6.0eabi-gcc --sysroot=/opt/qnx660/target/qnx6 -Wl,-E -o perl perlmain.o libperl.a
written lib/Config.pod
make2: Leaving directory `/home/cross/perl-5.24.0'
libperl.a(pp.o): In function `Perl_pp_crypt': pp.c:(.text+0xffd8): warning: The 'crypt' function has been deprecated in libc. Link against liblogin for extended algorithm support.
libperl.a(toke.o): In function `Perl_scan_num':
toke.c:(.text+0x27b82): undefined reference to `pow'
libperl.a(util.o): In function `Perl_drand48_r':
util.c:(.text+0xa36e): undefined reference to `ldexp'
libperl.a(sv.o): In function `S_hextract':
sv.c:(.text+0x13ca0): undefined reference to `frexp'
.
.
time64.c:(.text+0x3482): undefined reference to `floor'
time64.c:(.text+0x349c): undefined reference to `ceil'
time64.c:(.text+0x3522): undefined reference to `fmod'
time64.c:(.text+0x359c): undefined reference to `floor'
time64.c:(.text+0x37e6): undefined reference to `ceil'
collect2: error: ld returned 1 exit status
make: *** perl Error 1

could it be because i might have referenced wrong path for libraries in -Dsysroot option?