diff --git a/src/Processors/QueryPlan/ReadFromMergeTree.cpp b/src/Processors/QueryPlan/ReadFromMergeTree.cpp
index f8b41104130..107d2d5517e 100644
--- a/src/Processors/QueryPlan/ReadFromMergeTree.cpp
+++ b/src/Processors/QueryPlan/ReadFromMergeTree.cpp
@@ -1,10 +1,12 @@
 #include <algorithm>
 #include <functional>
 #include <iterator>
+#include <limits>
 #include <memory>
 #include <numeric>
 #include <queue>
 #include <stdexcept>
+#include <unordered_map>
 #include <IO/Operators.h>
 #include <Interpreters/Context.h>
 #include <Interpreters/ExpressionAnalyzer.h>
@@ -1336,21 +1338,37 @@ bool ReadFromMergeTree::requestOutputEachPartitionThroughSeparatePort()
             "Independent aggregation by partitions won't be used because there are too many of them: {}. You can increase "
             "max_number_of_partitions_for_independent_aggregation (current value is {}) or set "
             "force_aggregate_partitions_independently to suppress this check",
-            settings.max_number_of_partitions_for_independent_aggregation,
-            partitions_cnt);
+            partitions_cnt,
+            settings.max_number_of_partitions_for_independent_aggregation);
         return false;
     }
 
-    /// todo: check how big is the difference in the number of rows between parts and disable optimization if it is > 2.
-    /*if (!settings.force_aggregate_partitions_independently)
+    if (!settings.force_aggregate_partitions_independently)
     {
-        LOG_TRACE(
-            log,
-            "Independent aggregation by partitions won't be used because there are too big skew in the number of rows between partitions: "
-            "{} {} ."
-            "You can set force_aggregate_partitions_independently to suppress this check");
-        return false;
-    }*/
+        std::unordered_map<String, size_t> partition_rows;
+        for (const auto & part : prepared_parts)
+            partition_rows[part->info.partition_id] += part->rows_count;
+        size_t sum_rows = 0;
+        size_t max_rows = 0;
+        for (const auto & [_, rows] : partition_rows)
+        {
+            sum_rows += rows;
+            max_rows = std::max(max_rows, rows);
+        }
+
+        /// Merging shouldn't take more time than preaggregation in normal cases. And exec time is proportional to the amount of data.
+        /// We assume that exec time of independent aggr is proportional to the maximum of sizes and
+        /// exec time of ordinary aggr is proportional to sum of sizes divided by number of threads and multiplied by two (preaggregation + merging).
+        const size_t avg_rows_in_partition = sum_rows / settings.max_threads;
+        if (max_rows > avg_rows_in_partition * 2)
+        {
+            LOG_TRACE(
+                log,
+                "Independent aggregation by partitions won't be used because there are too big skew in the number of rows between "
+                "partitions. You can set force_aggregate_partitions_independently to suppress this check");
+            return false;
+        }
+    }
 
     return output_each_partition_through_separate_port = true;
 }
diff --git a/tests/queries/0_stateless/02521_aggregation_by_partitions.reference b/tests/queries/0_stateless/02521_aggregation_by_partitions.reference
index 121ebd52e5a..4a0967fb8ba 100644
--- a/tests/queries/0_stateless/02521_aggregation_by_partitions.reference
+++ b/tests/queries/0_stateless/02521_aggregation_by_partitions.reference
@@ -203,3 +203,6 @@ Skip merging: 0
 Skip merging: 1
 Skip merging: 0
 Skip merging: 1
+Skip merging: 0
+Skip merging: 0
+Skip merging: 0
diff --git a/tests/queries/0_stateless/02521_aggregation_by_partitions.sql b/tests/queries/0_stateless/02521_aggregation_by_partitions.sql
index 919ac374024..1c139e94591 100644
--- a/tests/queries/0_stateless/02521_aggregation_by_partitions.sql
+++ b/tests/queries/0_stateless/02521_aggregation_by_partitions.sql
@@ -170,3 +170,39 @@ select replaceRegexpOne(explain, '^[ ]*(.*)', '\\1') from (
 ) where explain like '%Skip merging: %';
 
 drop table t14;
+
+-- to few partitions --
+create table t15(a UInt32, b UInt32) engine=MergeTree order by a partition by a < 90;
+
+insert into t15 select number, number from numbers_mt(100);
+
+select replaceRegexpOne(explain, '^[ ]*(.*)', '\\1') from (
+    explain actions=1 select a from t15 group by a
+) where explain like '%Skip merging: %'
+settings force_aggregate_partitions_independently = 0;
+
+drop table t15;
+
+-- to many partitions --
+create table t16(a UInt32, b UInt32) engine=MergeTree order by a partition by a % 16;
+
+insert into t16 select number, number from numbers_mt(100);
+
+select replaceRegexpOne(explain, '^[ ]*(.*)', '\\1') from (
+    explain actions=1 select a from t16 group by a
+) where explain like '%Skip merging: %'
+settings force_aggregate_partitions_independently = 0, max_number_of_partitions_for_independent_aggregation = 4;
+
+drop table t16;
+
+-- to big skew --
+create table t17(a UInt32, b UInt32) engine=MergeTree order by a partition by a < 90;
+
+insert into t17 select number, number from numbers_mt(100);
+
+select replaceRegexpOne(explain, '^[ ]*(.*)', '\\1') from (
+    explain actions=1 select a from t17 group by a
+) where explain like '%Skip merging: %'
+settings force_aggregate_partitions_independently = 0, max_threads = 4;
+
+drop table t17;