diff --git a/R/adjacency.R b/R/adjacency.R
index 65b4eb21411..10497e4f3ff 100644
--- a/R/adjacency.R
+++ b/R/adjacency.R
@@ -494,8 +494,9 @@ graph.adjacency.sparse <- function(
   }
 
   vc <- nrow(adjmatrix)
-  # Exit early for empty graphs
-  if (vc == 1 || Matrix::nnzero(adjmatrix) == 0) {
+  # Exit early for empty graphs. Use na.counted = TRUE so that NA entries
+  # (which are stored explicitly) do not cause nnzero() to return NA.
+  if (vc == 1 || Matrix::nnzero(adjmatrix, na.counted = TRUE) == 0) {
     return(make_empty_graph(n = vc, directed = (mode == "directed")))
   }
 
diff --git a/R/utils-assert-args.R b/R/utils-assert-args.R
index cfb2ddf3025..c80e7cb9cfd 100644
--- a/R/utils-assert-args.R
+++ b/R/utils-assert-args.R
@@ -66,9 +66,17 @@ igraph_match_arg <- function(
 #' @importFrom rlang caller_env
 ensure_no_na <- function(x, what, mode = "", call = caller_env()) {
   if (mode == "upper") {
-    x <- x[upper.tri(x)]
+    if (inherits(x, "sparseMatrix")) {
+      x <- Matrix::triu(x)@x
+    } else {
+      x <- x[upper.tri(x)]
+    }
   } else if (mode == "lower") {
-    x <- x[lower.tri(x)]
+    if (inherits(x, "sparseMatrix")) {
+      x <- Matrix::tril(x)@x
+    } else {
+      x <- x[lower.tri(x)]
+    }
   }
   if (anyNA(x)) {
     cli::cli_abort(
diff --git a/tests/testthat/test-adjacency.R b/tests/testthat/test-adjacency.R
index c4f2669202b..b43e54c3450 100644
--- a/tests/testthat/test-adjacency.R
+++ b/tests/testthat/test-adjacency.R
@@ -879,3 +879,37 @@ test_that("graph_from_adjacency Na check for upper/lower", {
     )
   )
 })
+
+test_that("graph_from_adjacency NA check for upper/lower with sparse matrices", {
+  # Sparse matrix with NA only in upper triangle: mode="upper" should error,
+  # mode="lower" should succeed
+  sp <- Matrix::sparseMatrix(
+    i = c(1, 2, 1),
+    j = c(2, 1, 1),
+    x = c(NA_real_, 1, 1),
+    dims = c(3, 3)
+  )
+  expect_error(
+    graph_from_adjacency_matrix(sp, mode = "upper", weighted = TRUE),
+    "contains NAs"
+  )
+  expect_no_error(
+    graph_from_adjacency_matrix(sp, mode = "lower", weighted = TRUE)
+  )
+
+  # Sparse matrix with NA only in lower triangle: mode="lower" should error,
+  # mode="upper" should succeed
+  sp2 <- Matrix::sparseMatrix(
+    i = c(2, 1, 1),
+    j = c(1, 2, 1),
+    x = c(NA_real_, 1, 1),
+    dims = c(3, 3)
+  )
+  expect_error(
+    graph_from_adjacency_matrix(sp2, mode = "lower", weighted = TRUE),
+    "contains NAs"
+  )
+  expect_no_error(
+    graph_from_adjacency_matrix(sp2, mode = "upper", weighted = TRUE)
+  )
+})