diff --git a/dorado/alignment/Minimap2Aligner.cpp b/dorado/alignment/Minimap2Aligner.cpp
index f7346576..217625e5 100644
--- a/dorado/alignment/Minimap2Aligner.cpp
+++ b/dorado/alignment/Minimap2Aligner.cpp
@@ -223,7 +223,7 @@ std::vector<BamPtr> Minimap2Aligner::align(bam1_t* irecord, mm_tbuf_t* buf) {
         add_sa_tag(record, reg, hits, j, static_cast<int>(l_seq), mm_index, use_hard_clip);
 
         // Remove MM/ML/MN tags if secondary alignment and soft clipping is not enabled.
-        if ((flag & BAM_FSUPPLEMENTARY) && !(mm_map_opts.flag & MM_F_SOFTCLIP)) {
+        if ((flag & (BAM_FSUPPLEMENTARY | BAM_FSECONDARY)) && !(mm_map_opts.flag & MM_F_SOFTCLIP)) {
             if (auto tag = bam_aux_get(record, "MM"); tag != nullptr) {
                 bam_aux_del(record, tag);
             }
diff --git a/tests/AlignerTest.cpp b/tests/AlignerTest.cpp
index 96c306bd..b0e81026 100644
--- a/tests/AlignerTest.cpp
+++ b/tests/AlignerTest.cpp
@@ -197,19 +197,33 @@ TEST_CASE("AlignerTest: Check modbase tags are removed for secondary alignments"
     options.soft_clipping = GENERATE(true, false);
     dorado::HtsReader reader(query.string(), std::nullopt);
     auto bam_records = RunAlignmentPipeline(reader, ref.string(), options, 10);
-    REQUIRE(bam_records.size() == 2);
+    REQUIRE(bam_records.size() == 3);
 
-    bam1_t* rec = bam_records[1].get();
+    bam1_t* primary_rec = bam_records[0].get();
+    bam1_t* secondary_rec = bam_records[1].get();
+    bam1_t* supplementary_rec = bam_records[2].get();
 
     // Check aux tags.
     if (options.soft_clipping) {
-        CHECK(bam_aux_get(rec, "MM") != nullptr);
-        CHECK(bam_aux_get(rec, "ML") != nullptr);
-        CHECK(bam_aux_get(rec, "MN") != nullptr);
+        CHECK(bam_aux_get(primary_rec, "MM") != nullptr);
+        CHECK(bam_aux_get(primary_rec, "ML") != nullptr);
+        CHECK(bam_aux_get(primary_rec, "MN") != nullptr);
+        CHECK(bam_aux_get(secondary_rec, "MM") != nullptr);
+        CHECK(bam_aux_get(secondary_rec, "ML") != nullptr);
+        CHECK(bam_aux_get(secondary_rec, "MN") != nullptr);
+        CHECK(bam_aux_get(supplementary_rec, "MM") != nullptr);
+        CHECK(bam_aux_get(supplementary_rec, "ML") != nullptr);
+        CHECK(bam_aux_get(supplementary_rec, "MN") != nullptr);
     } else {
-        CHECK(bam_aux_get(rec, "MM") == nullptr);
-        CHECK(bam_aux_get(rec, "ML") == nullptr);
-        CHECK(bam_aux_get(rec, "MN") == nullptr);
+        CHECK(bam_aux_get(primary_rec, "MM") != nullptr);
+        CHECK(bam_aux_get(primary_rec, "ML") != nullptr);
+        CHECK(bam_aux_get(primary_rec, "MN") != nullptr);
+        CHECK(bam_aux_get(secondary_rec, "MM") == nullptr);
+        CHECK(bam_aux_get(secondary_rec, "ML") == nullptr);
+        CHECK(bam_aux_get(secondary_rec, "MN") == nullptr);
+        CHECK(bam_aux_get(supplementary_rec, "MM") == nullptr);
+        CHECK(bam_aux_get(supplementary_rec, "ML") == nullptr);
+        CHECK(bam_aux_get(supplementary_rec, "MN") == nullptr);
     }
 }
 
diff --git a/tests/data/aligner_test/supplementary_basecall_target.fa b/tests/data/aligner_test/supplementary_basecall_target.fa
index adecdce6..4282443c 100644
--- a/tests/data/aligner_test/supplementary_basecall_target.fa
+++ b/tests/data/aligner_test/supplementary_basecall_target.fa
@@ -1,4 +1,6 @@
 >read1 999
 CCCTTTTTGCCCCTTTACGCCGCACCTAGCATATGCGCCTGCCACTTGCAGCTTTCCCGCCCCTGCCCGCCTGCCCACCCCTTGCCGCCTCCTTATGCGCCGCCCCGCCCACCCCCGCCCACCCACCGCCCCACGCTTCCCCCACCCGCCGCCCACGCGCATCGCCCGCCCCCCCCGCCCCACCCGCCCACCGCCCTGTCCAAAGCCCGCCCCACGCCCGGCCCGCGCCCGCCAGCCCCGCCCCGTGGCCGCCGCCCCCGCCCGCCCCCCACCCGCCCCCCTACCTGCCCGCCTGGCCGCCGCCTCCCATCCCACCCGCCACCCGCCCCCTGTGCCCCACTTCCAGCCCGGCCGCCCATCCCCGCCCCCCCCCCCCACCCACCGCCCCCCGGCCAGCCCCCGCCCCCGCCCCGCCCGCCCGGCGCCGGCCCCATGCCCCCACCCCGCTGCCCCGCGCCCCCGCCCAGCCACACCCACCCCGCCGCCCCACCCGCCCCCACCGGCCCCGCCCGGCGCAGCCCGGCAGCTTCCCCCGCCCACGCCGCCCCCTTGCCAGCCCACCCCGCAGCTCACCCACCAGCCCATCCCGCTCCCCCGGCGCCCCAGCCGCCCGCCCACCCGCCGCGCACCCGCCCCCGCCCGCTCCCCCCCGCCCACCCGCCCGCCTCGCCCATCTGCTCCCCCCACCCACCCCCGCGCCCATGCGCCCCCCGCCCACCCCGCGCCCACCCGCCCCCCGCCCCACCCACCCACCCCGCCCCGCCCCACTTGCCCCCACGCCCCCGCCCCCCGCCGCCGCCCTCCCACACACGCTTCCCAGCCCGCTTCGCACAGCGCCTACCGCCGCCCCACCCGCCCCTTAAAAGCCACCGGCGCCCGCGCACCCACCCCGCCATCCAGCAGCCAACCAGCCCTTGCTTCCCCATACTTGTAAAGCTTCCCCGCACCCGCCCGCCTTCCACCCACCCACCGCCCCCCCGGCCCGCCGCCCGGCCTCGC
+>read3 999
+CCCTTTTTGCCCCTTTACGCCGCACCTAGCATATGCGCCTGCCACTTGCAGCTTTCCCGCCCCTGCCCGCCTGCCCACCCCTTGCCGCCTCCTTATGCGCCGCCCCGCCCACCCCCGCCCACCCACCGCCCCACGCTTCCCCCACCCGCCGCCCACGCGCATCGCCCGCCCCCCCCGCCCCACCCGCCCACCGCCCTGTCCAAAGCCCGCCCCACGCCCGGCCCGCGCCCGCCAGCCCCGCCCCGTGGCCGCCGCCCCCGCCCGCCCCCCACCCGCCCCCCTACCTGCCCGCCTGGCCGCCGCCTCCCATCCCACCCGCCACCCGCCCCCTGTGCCCCACTTCCAGCCCGGCCGCCCATCCCCGCCCCCCCCCCCCACCCACCGCCCCCCGGCCAGCCCCCGCCCCCGCCCCGCCCGCCCGGCGCCGGCCCCATGCCCCCACCCCGCTGCCCCGCGCCCCCGCCCAGCCACACCCACCCCGCCGCCCCACCCGCCCCCACCGGCCCCGCCCGGCGCAGCCCGGCAGCTTCCCCCGCCCACGCCGCCCCCTTGCCAGCCCACCCCGCAGCTCACCCACCAGCCCATCCCGCTCCCCCGGCGCCCCAGCCGCCCGCCCACCCGCCGCGCACCCGCCCCCGCCCGCTCCCCCCCGCCCACCCGCCCGCCTCGCCCATCTGCTCCCCCCACCCACCCCCGCGCCCATGCGCCCCCCGCCCACCCCGCGCCCACCCGCCCCCCGCCCCACCCACCCACCCCGCCCCGCCCCACTTGCCCCCACGCCCCCGCCCCCCGCCGCCGCCCTCCCACACACGCTTCCCAGCCCGCTTCGCACAGCGCCTACCGCCGCCCCACCCGCCCCTTAAAAGCCACCGGCGCCCGCGCACCCACCCCGCCATCCAGCAGCCAACCAGCCCTTGCTTCCCCATACTTGTAAAGCTTCCCCGCACCCGCCCGCCTTCCACCCACCCACCGCCCCCCCGGCCCGCCGCCCGGCCTCGC
 >read2 899
 CCGGCCCCGGCCCAGCCTTGCCCGCCTTCTCGAAGCGCCGCCGCGCCTCCAGCCCAGCCCGCCCACCCTCGCCCGCTTGCCCCCGGCTCGCGCTCCAGGCGCCCGGCCCCGGCCCCGCCCGCGCTCTGCCATTTCCACTTCCCACCGGCCAAAGCCCGCCGGCATCCCGCGCGCCCGCACAAGCCAAGCTTCCCCGGCTTGGCGCCATTTAAGCAAAAGCCGCCCGCCAACGCCAGCGCCCGGCGCCCGGCCCGCCACCGGCAGCGCCGCCCTTTCCAGCCCGGCGCTGGCCATCGGCCAGCGCACCACGAAGCCAGCCCACCGCCAGCCCGCCAAAGCCGCTCCCACAAGCCAAAGCCCGCCCACCCCCAGCCACCCATACCCCGCTCGCCCGCCAGCTTCTGTATGCCCACCCAGCGCACTTGCTTTCCACCCCCACCCCCGCCCCGCGCCCGCCCGCCCGCCACCCCTGCCCCGCCCCCCGCCGCTGCCTTACCGCTGCCCCAAAGCGCCCTTCCAGCACTTCCTTAGCCACCCTTTTTAGCTTCACTTCCACCTACCGCTTGCCGCCGGCTGCTTCCCCGCCCATCCCACCGCACCCGCCCGCGCCTTATGCGCACCGCCCGCGCCCGGCCTGCAAGCCAGCTTCGCGCGCCCGCTTCCACCACCCCCGCCAGCCCGCTTCCTGCTTGCCCCCGCCGCACCGCCCACCCACCCCCACCGGCCAGCGCTCATATGCCCCCGCCGCACCAGCACGCCACCGCCCGCCTCCTTCGCCAGCCCGCCCACCCGCCGCCCAGCCACCGCACCCACTCAAGGGGTCGCCTCTCATGCGCATCATGCGCAAAAAAAAAAACGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAA