diff --git a/rust/lance-index/src/vector/hnsw/builder.rs b/rust/lance-index/src/vector/hnsw/builder.rs
index 66e1bee758f..c7648fa746f 100644
--- a/rust/lance-index/src/vector/hnsw/builder.rs
+++ b/rust/lance-index/src/vector/hnsw/builder.rs
@@ -19,7 +19,6 @@ use std::cmp::min;
 use std::collections::{BinaryHeap, HashMap, VecDeque};
 use std::fmt::Debug;
 use std::iter;
-use std::sync::atomic::{AtomicUsize, Ordering};
 use std::sync::Arc;
 use std::sync::RwLock;
 use tracing::instrument;
@@ -307,10 +306,10 @@ impl HNSW {
             .inner
             .level_count
             .iter()
-            .chain(iter::once(&AtomicUsize::new(0)))
-            .scan(0, |state, x| {
+            .chain(iter::once(&0usize))
+            .scan(0usize, |state, &count| {
                 let start = *state;
-                *state += x.load(Ordering::Relaxed);
+                *state += count;
                 Some(start)
             })
             .collect();
@@ -327,7 +326,7 @@ struct HnswBuilder {
     params: HnswBuildParams,
 
     nodes: Arc<Vec<RwLock<GraphBuilderNode>>>,
-    level_count: Vec<AtomicUsize>,
+    level_count: Vec<usize>,
 
     entry_point: u32,
 
@@ -349,7 +348,7 @@ impl HnswBuilder {
     }
 
     fn num_nodes(&self, level: usize) -> usize {
-        self.level_count[level].load(Ordering::Relaxed)
+        self.level_count[level]
     }
 
     fn nodes(&self) -> Arc<Vec<RwLock<GraphBuilderNode>>> {
@@ -361,9 +360,7 @@ impl HnswBuilder {
         let len = storage.len();
         let max_level = params.max_level;
 
-        let level_count = (0..max_level)
-            .map(|_| AtomicUsize::new(0))
-            .collect::<Vec<_>>();
+        let level_count = vec![0usize; max_level as usize];
 
         let visited_generator_queue = Arc::new(ArrayQueue::new(get_num_compute_intensive_cpus()));
         for _ in 0..get_num_compute_intensive_cpus() {
@@ -445,8 +442,6 @@ impl HnswBuilder {
         {
             let mut current_node = nodes[node as usize].write().unwrap();
             for level in (0..=target_level).rev() {
-                self.level_count[level as usize].fetch_add(1, Ordering::Relaxed);
-
                 let neighbors = self.search_level(&ep, level, &dist_calc, nodes, visited_generator);
                 for neighbor in &neighbors {
                     current_node.add_neighbor(neighbor.id, neighbor.dist, level);
@@ -525,6 +520,17 @@ impl HnswBuilder {
         *neighbors_ranked = select_neighbors_heuristic(storage, &level_neighbors, m_max);
         builder_node.update_from_ranked_neighbors(level);
     }
+
+    fn compute_level_count(&self) -> Vec<usize> {
+        let mut level_count = vec![0usize; self.max_level() as usize];
+        for node in self.nodes.iter() {
+            let levels = node.read().unwrap().level_neighbors.len();
+            for count in level_count.iter_mut().take(levels) {
+                *count += 1;
+            }
+        }
+        level_count
+    }
 }
 
 // View of a level in HNSW graph.
@@ -666,7 +672,7 @@ impl IvfSubIndex for HNSW {
         let inner = HnswBuilder {
             params: hnsw_metadata.params,
             nodes: Arc::new(nodes.into_iter().map(RwLock::new).collect()),
-            level_count: level_count.into_iter().map(AtomicUsize::new).collect(),
+            level_count,
             entry_point: hnsw_metadata.entry_point,
             visited_generator_queue,
         };
@@ -763,34 +769,37 @@ impl IvfSubIndex for HNSW {
     where
         Self: Sized,
     {
-        let inner = HnswBuilder::with_params(params, storage);
-        let hnsw = Self {
-            inner: Arc::new(inner),
-        };
+        let mut inner = HnswBuilder::with_params(params, storage);
 
         log::debug!(
             "Building HNSW graph: num={}, max_levels={}, m={}, ef_construction={}, distance_type:{}",
             storage.len(),
-            hnsw.inner.params.max_level,
-            hnsw.inner.params.m,
-            hnsw.inner.params.ef_construction,
+            inner.params.max_level,
+            inner.params.m,
+            inner.params.ef_construction,
             storage.distance_type(),
         );
 
         if storage.is_empty() {
-            return Ok(hnsw);
+            return Ok(Self {
+                inner: Arc::new(inner),
+            });
         }
 
         let len = storage.len();
-        hnsw.inner.level_count[0].fetch_add(1, Ordering::Relaxed);
         (1..len).into_par_iter().for_each_init(
             || VisitedGenerator::new(len),
             |visited_generator, node| {
-                hnsw.inner.insert(node as u32, visited_generator, storage);
+                inner.insert(node as u32, visited_generator, storage);
             },
         );
+        inner.level_count = inner.compute_level_count();
 
-        assert_eq!(hnsw.inner.level_count[0].load(Ordering::Relaxed), len);
+        let hnsw = Self {
+            inner: Arc::new(inner),
+        };
+
+        assert_eq!(hnsw.inner.level_count[0], len);
         Ok(hnsw)
     }
 
@@ -945,4 +954,19 @@ mod tests {
             .unwrap();
         assert_eq!(builder_results, loaded_results);
     }
+
+    #[test]
+    fn test_level_offsets_match_batch_rows() {
+        const DIM: usize = 16;
+        const TOTAL: usize = 512;
+        let data = generate_random_array(TOTAL * DIM);
+        let fsl = FixedSizeListArray::try_new_from_values(data, DIM as i32).unwrap();
+        let store = FlatFloatStorage::new(fsl, DistanceType::L2);
+        let hnsw = HNSW::index_vectors(&store, HnswBuildParams::default()).unwrap();
+        let metadata = hnsw.metadata();
+        let batch = hnsw.to_batch().unwrap();
+
+        assert_eq!(metadata.level_offsets.len(), hnsw.max_level() as usize + 1);
+        assert_eq!(*metadata.level_offsets.last().unwrap(), batch.num_rows());
+    }
 }