diff --git a/.ci/test_r_package_valgrind.sh b/.ci/test_r_package_valgrind.sh
index 50d65bc340c2..fa4d6b3e6357 100755
--- a/.ci/test_r_package_valgrind.sh
+++ b/.ci/test_r_package_valgrind.sh
@@ -39,28 +39,28 @@ if [[ ${bytes_indirectly_lost} -gt 0 ]]; then
 fi
 
 # one error caused by a false positive between valgrind and openmp is allowed
-# ==1312== 352 bytes in 1 blocks are possibly lost in loss record 146 of 2,458
-# ==1312==    at 0x483DD99: calloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
-# ==1312==    by 0x40149CA: allocate_dtv (dl-tls.c:286)
-# ==1312==    by 0x40149CA: _dl_allocate_tls (dl-tls.c:532)
-# ==1312==    by 0x5702322: allocate_stack (allocatestack.c:622)
-# ==1312==    by 0x5702322: pthread_create@@GLIBC_2.2.5 (pthread_create.c:660)
-# ==1312==    by 0x56D0DDA: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
-# ==1312==    by 0x56C88E0: GOMP_parallel (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
-# ==1312==    by 0x154351B8: LGBM_DatasetCreateFromCSC (c_api.cpp:1286)
-# ==1312==    by 0x1545789C: LGBM_DatasetCreateFromCSC_R (lightgbm_R.cpp:91)
-# ==1312==    by 0x4941E2F: R_doDotCall (dotcode.c:634)
-# ==1312==    by 0x494CCC6: do_dotcall (dotcode.c:1281)
-# ==1312==    by 0x499FB01: bcEval (eval.c:7078)
-# ==1312==    by 0x498B67F: Rf_eval (eval.c:727)
-# ==1312==    by 0x498E414: R_execClosure (eval.c:1895)
+# ==2063== 336 bytes in 1 blocks are possibly lost in loss record 153 of 2,709
+# ==2063==    at 0x483DD99: calloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
+# ==2063==    by 0x40149CA: allocate_dtv (dl-tls.c:286)
+# ==2063==    by 0x40149CA: _dl_allocate_tls (dl-tls.c:532)
+# ==2063==    by 0x5702322: allocate_stack (allocatestack.c:622)
+# ==2063==    by 0x5702322: pthread_create@@GLIBC_2.2.5 (pthread_create.c:660)
+# ==2063==    by 0x56D0DDA: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
+# ==2063==    by 0x56C88E0: GOMP_parallel (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
+# ==2063==    by 0x1544D29C: LGBM_DatasetCreateFromCSC (c_api.cpp:1286)
+# ==2063==    by 0x1546F980: LGBM_DatasetCreateFromCSC_R (lightgbm_R.cpp:91)
+# ==2063==    by 0x4941E2F: R_doDotCall (dotcode.c:634)
+# ==2063==    by 0x494CCC6: do_dotcall (dotcode.c:1281)
+# ==2063==    by 0x499FB01: bcEval (eval.c:7078)
+# ==2063==    by 0x498B67F: Rf_eval (eval.c:727)
+# ==2063==    by 0x498E414: R_execClosure (eval.c:1895)
 bytes_possibly_lost=$(
     cat ${VALGRIND_LOGS_FILE} \
     | grep -E "possibly lost\: .*" \
     | sed 's/^.*possibly lost\: \(.*\) bytes.*$/\1/' \
     | tr -d ","
 )
-if [[ ${bytes_possibly_lost} -gt 352 ]]; then
+if [[ ${bytes_possibly_lost} -gt 336 ]]; then
     echo "valgrind found ${bytes_possibly_lost} bytes possibly lost"
     exit -1
 fi